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-rw-r--r--gnu/packages/bioinformatics.scm3118
1 files changed, 1393 insertions, 1725 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aad13317b8..8c3be14e65 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -265,21 +265,21 @@ structure of the predicted RNA.")
`("PATH" ":" prefix (,path))
`("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))))))))
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("libtool" ,libtool)
- ("zlib" ,zlib)
- ("python-nose" ,python2-nose)
- ("python-pysam" ,python2-pysam)))
- (inputs
- `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
- ("samtools" ,samtools)
- ("bwa" ,bwa)
- ("grep" ,grep)
- ("sed" ,sed)
- ("coreutils" ,coreutils)))
+ (list autoconf
+ automake
+ libtool
+ zlib
+ python2-nose
+ python2-pysam))
+ (inputs
+ (list htslib-1.3 ; At least one test fails on htslib-1.4+.
+ samtools
+ bwa
+ grep
+ sed
+ coreutils))
(propagated-inputs
- `(("python-numpy" ,python2-numpy)))
+ (list python2-numpy))
(home-page "https://ecogenomics.github.io/BamM/")
(synopsis "Metagenomics-focused BAM file manipulator")
(description
@@ -314,7 +314,7 @@ instance, it implements several methods to assess contig-wise read coverage.")
"-Wl,-rpath="
(assoc-ref outputs "out") "/lib/bamtools"))
#t)))))
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
(home-page "https://github.com/pezmaster31/bamtools")
(synopsis "C++ API and command-line toolkit for working with BAM data")
(description
@@ -350,7 +350,7 @@ BAM files.")
(copy-recursively (assoc-ref inputs "libstatgen")
"../libStatGen"))))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
`(("libstatgen"
,(origin
@@ -399,11 +399,9 @@ single executable called @code{bam}.")
(("/bin/bash") (which "bash")))
#t)))))
(native-inputs
- `(("htslib" ,htslib)
- ("perl" ,perl)))
+ (list htslib perl))
(inputs
- `(("gsl" ,gsl)
- ("zlib" ,zlib)))
+ (list gsl zlib))
(home-page "https://samtools.github.io/bcftools/")
(synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
(description
@@ -432,8 +430,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
#t))))
(build-system gnu-build-system)
(native-inputs
- `(("htslib" ,htslib-1.10)
- ("perl" ,perl)))))
+ (list htslib-1.10 perl))))
(define-public bedops
(package
@@ -518,8 +515,7 @@ computational cluster.")
(native-inputs
`(("python" ,python-wrapper)))
(inputs
- `(("samtools" ,samtools)
- ("zlib" ,zlib)))
+ (list samtools zlib))
(home-page "https://github.com/arq5x/bedtools2")
(synopsis "Tools for genome analysis and arithmetic")
(description
@@ -567,8 +563,7 @@ BED, GFF/GTF, VCF.")
(native-inputs
`(("python" ,python-wrapper)))
(inputs
- `(("samtools" ,samtools)
- ("zlib" ,zlib)))))
+ (list samtools zlib))))
(define-public pbcopper
;; This is the latest commit at the time of this writing.
@@ -595,10 +590,9 @@ BED, GFF/GTF, VCF.")
(substitute* "meson.build"
(("-msse4.1") "")))))))
(inputs
- `(("boost" ,boost)))
+ (list boost))
(native-inputs
- `(("googletest" ,googletest)
- ("pkg-config" ,pkg-config)))
+ (list googletest pkg-config))
(home-page "https://github.com/PacificBiosciences/pbcopper")
(synopsis "Data structures, algorithms, and utilities for PacBio C++ applications")
(description
@@ -639,12 +633,9 @@ and utilities for PacBio C++ applications.")
(string-append "'" (which "sh") "'"))))))))
;; These libraries are listed as "Required" in the pkg-config file.
(propagated-inputs
- `(("htslib" ,htslib)
- ("pbcopper" ,pbcopper)
- ("zlib" ,zlib)))
+ (list htslib pbcopper zlib))
(inputs
- `(("boost" ,boost)
- ("samtools" ,samtools)))
+ (list boost samtools))
(native-inputs
`(("googletest" ,googletest)
("pkg-config" ,pkg-config)
@@ -676,10 +667,9 @@ Non-PacBio BAMs will cause exceptions to be thrown.")
"1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
(build-system gnu-build-system)
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)))
+ (list autoconf automake))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/nh13/pbgzip")
(synopsis "Parallel Block GZIP")
(description "This package implements parallel block gzip. For many
@@ -741,14 +731,9 @@ libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n"
#:tests? #f
#:configure-flags '("-Dtests=false")))
(inputs
- `(("boost" ,boost)
- ("hdf5" ,hdf5)
- ("htslib" ,htslib)
- ("pbbam" ,pbbam)
- ("zlib" ,zlib)))
+ (list boost hdf5 htslib pbbam zlib))
(native-inputs
- `(("googletest" ,googletest)
- ("pkg-config" ,pkg-config)))
+ (list googletest pkg-config))
(home-page "https://github.com/PacificBiosciences/blasr_libcpp")
(synopsis "Library for analyzing PacBio genomic sequences")
(description
@@ -788,13 +773,9 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), "
#:tests? #f
#:configure-flags '("-Dtests=false")))
(inputs
- `(("boost" ,boost)
- ("blasr-libcpp" ,blasr-libcpp)
- ("hdf5" ,hdf5)
- ("pbbam" ,pbbam)
- ("zlib" ,zlib)))
+ (list boost blasr-libcpp hdf5 pbbam zlib))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "https://github.com/PacificBiosciences/blasr")
(synopsis "PacBio long read aligner")
(description
@@ -830,14 +811,14 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), "
"Ribotaper.sh")))
#t)))))
(inputs
- `(("bedtools" ,bedtools-2.18)
- ("samtools" ,samtools-0.1)
- ("r-minimal" ,r-minimal)
- ("r-foreach" ,r-foreach)
- ("r-xnomial" ,r-xnomial)
- ("r-domc" ,r-domc)
- ("r-multitaper" ,r-multitaper)
- ("r-seqinr" ,r-seqinr)))
+ (list bedtools-2.18
+ samtools-0.1
+ r-minimal
+ r-foreach
+ r-xnomial
+ r-domc
+ r-multitaper
+ r-seqinr))
(home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
(synopsis "Define translated ORFs using ribosome profiling data")
(description
@@ -878,13 +859,10 @@ provides the Ribotaper pipeline.")
(string-append line "\n"
prefix "scripts=['scripts/TE.py'],\n"))))))))
(inputs
- `(("python-numpy" ,python2-numpy)
- ("python-matplotlib" ,python2-matplotlib)
- ("python-scipy" ,python2-scipy)
- ("python-statsmodels" ,python2-statsmodels)))
+ (list python2-numpy python2-matplotlib python2-scipy
+ python2-statsmodels))
(native-inputs
- `(("python-mock" ,python2-mock)
- ("python-nose" ,python2-nose)))
+ (list python2-mock python2-nose))
(home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
(synopsis "Detect translation efficiency changes from ribosome footprints")
(description "RiboDiff is a statistical tool that detects the protein
@@ -910,9 +888,9 @@ independently with transcriptional regulation.")
"1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm"))))
(build-system gnu-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("bison" ,bison)))
+ (list bison))
(arguments
`(#:tests? #f ; There are no tests to run.
;; Bison must generate files, before other targets can build.
@@ -951,11 +929,9 @@ intended to behave exactly the same as the original BWK awk.")
"0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk"))))
(build-system python-build-system)
(native-inputs
- `(("python-setuptools-scm" ,python-setuptools-scm)))
+ (list python-setuptools-scm))
(propagated-inputs
- `(("python-humanize" ,python-humanize)
- ("python-requests" ,python-requests)
- ("python-six" ,python-six)))
+ (list python-humanize python-requests python-six))
(home-page "https://pypi.org/project/htsget/")
(synopsis "Python API and command line interface for the GA4GH htsget API")
(description "This package is a client implementation of the GA4GH htsget
@@ -1018,20 +994,17 @@ servers supporting the protocol.")
(with-directory-excursion "/tmp/test"
(invoke "pytest" "-v" "--doctest-modules")))))))
(propagated-inputs
- `(("bedtools" ,bedtools)
- ("samtools" ,samtools)
- ("python-matplotlib" ,python-matplotlib)
- ("python-pysam" ,python-pysam)
- ("python-pyyaml" ,python-pyyaml)))
- (native-inputs
- `(("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-cython" ,python-cython)
- ("kentutils" ,kentutils) ; for bedGraphToBigWig
- ("python-six" ,python-six)
- ;; For the test suite.
- ("python-pytest" ,python-pytest)
- ("python-psutil" ,python-psutil)))
+ (list bedtools samtools python-matplotlib python-pysam
+ python-pyyaml))
+ (native-inputs
+ (list python-numpy
+ python-pandas
+ python-cython
+ kentutils ; for bedGraphToBigWig
+ python-six
+ ;; For the test suite.
+ python-pytest
+ python-psutil))
(home-page "https://pythonhosted.org/pybedtools/")
(synopsis "Python wrapper for BEDtools programs")
(description
@@ -1046,8 +1019,8 @@ Python.")
(package
(inherit pybedtools)
(native-inputs
- `(("python2-pathlib" ,python2-pathlib)
- ,@(package-native-inputs pybedtools))))))
+ (modify-inputs (package-native-inputs pybedtools)
+ (prepend python2-pathlib))))))
(define-public python-biom-format
(package
@@ -1098,19 +1071,16 @@ Python.")
(for-each (lambda (file) (chmod file #o644))
(find-files out "\\.gz"))))))))
(propagated-inputs
- `(("python-anndata" ,python-anndata)
- ("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)
- ("python-flake8" ,python-flake8)
- ("python-future" ,python-future)
- ("python-click" ,python-click)
- ("python-h5py" ,python-h5py)
- ("python-pandas" ,python-pandas)))
- (native-inputs
- `(("python-cython" ,python-cython)
- ("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-nose" ,python-nose)))
+ (list python-anndata
+ python-numpy
+ python-scipy
+ python-flake8
+ python-future
+ python-click
+ python-h5py
+ python-pandas))
+ (native-inputs
+ (list python-cython python-pytest python-pytest-cov python-nose))
(home-page "http://www.biom-format.org")
(synopsis "Biological Observation Matrix (BIOM) format utilities")
(description
@@ -1149,17 +1119,15 @@ e.g. microbiome samples, genomes, metagenomes.")
(with-directory-excursion "/tmp"
(invoke "pytest" "-v")))))))
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-nose" ,python-nose)
- ("python-pytest" ,python-pytest)))
+ (list python-cython python-nose python-pytest))
(inputs
`(("python" ,python-wrapper)))
(propagated-inputs
- `(("htslib" ,htslib) ; for bgzip, looked up in PATH
- ("samtools" ,samtools) ; looked up in PATH
- ("lz4" ,lz4) ; for lz4c
- ("python-click" ,python-click)
- ("python-numpy" ,python-numpy)))
+ (list htslib ; for bgzip, looked up in PATH
+ samtools ; looked up in PATH
+ lz4 ; for lz4c
+ python-click
+ python-numpy))
(home-page "https://github.com/mirnylab/pairtools")
(synopsis "Process mapped Hi-C data")
(description "Pairtools is a simple and fast command-line framework to
@@ -1226,12 +1194,9 @@ alignments and perform the following operations:
(find-files bin "\\.pl$"))
#t)))))))
(inputs
- `(("perl-module-build" ,perl-module-build)
- ("perl-data-stag" ,perl-data-stag)
- ("perl-libwww" ,perl-libwww)
- ("perl-uri" ,perl-uri)))
+ (list perl-module-build perl-data-stag perl-libwww perl-uri))
(native-inputs
- `(("perl-test-most" ,perl-test-most)))
+ (list perl-test-most))
(home-page "https://metacpan.org/release/BioPerl")
(synopsis "Bioinformatics toolkit")
(description
@@ -1259,11 +1224,9 @@ provide a coordinated and extensible framework to do computational biology.")
"0hjg0igfkpvh27zdkdr6pa7cqm9n6r7cwz0np74cl4wmawgvr9hj"))))
(build-system perl-build-system)
(native-inputs
- `(("perl-module-build" ,perl-module-build)
- ("pkg-config" ,pkg-config)))
+ (list perl-module-build pkg-config))
(propagated-inputs
- `(("bioperl-minimal" ,bioperl-minimal)
- ("htslib" ,htslib-1.9)))
+ (list bioperl-minimal htslib-1.9))
(home-page "https://metacpan.org/release/Bio-DB-HTS")
(synopsis "Perl interface to HTS library for DNA sequencing")
(description "This is a Perl interface to the HTS library for DNA
@@ -1289,7 +1252,7 @@ sequencing.")
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #t)))))
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(home-page "https://biopython.org/")
(synopsis "Tools for biological computation in Python")
(description
@@ -1363,7 +1326,7 @@ relying on a complex dependency tree.")
(when tests?
(invoke "./bin/biosoup_test")))))))
(native-inputs
- `(("googletest" ,googletest)))
+ (list googletest))
(home-page "https://github.com/rvaser/biosoup")
(synopsis "C++ support library for bioinformatics tools")
(description "Biosoup is a C++ collection of header-only data structures
@@ -1394,11 +1357,11 @@ used for storage and logging in bioinformatics tools.")
(when tests?
(invoke "./bin/bioparser_test")))))))
(inputs
- `(("biosoup" ,biosoup)))
+ (list biosoup))
(propagated-inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("googletest" ,googletest)))
+ (list googletest))
(home-page "https://github.com/rvaser/bioparser")
(synopsis "C++ library for parsing several formats in bioinformatics")
(description "Bioparser is a C++ header only parsing library for several
@@ -1448,12 +1411,9 @@ compressed files.")
("rust-serde" ,rust-serde-1)
("rust-seq-io" ,rust-seq-io-0.3))))
(inputs
- `(("bioparser" ,bioparser)
- ("biosoup" ,biosoup)))
+ (list bioparser biosoup))
(native-inputs
- `(("cmake" ,cmake)
- ("pkg-config" ,pkg-config)
- ("googletest" ,googletest)))
+ (list cmake pkg-config googletest))
(home-page "https://github.com/Kevinzjy/circtools")
(synopsis "Accelerating functions in CIRI toolkit")
(description "This package provides accelerated functions for the CIRI
@@ -1501,21 +1461,19 @@ consensus sequences.")
(substitute* "CIRI_long/main.py"
(("os.chmod\\(lib_path.*") "")))))))
(inputs
- `(("circtools" ,circtools)
- ("python-biopython" ,python-biopython)
- ("python-bwapy" ,python-bwapy)
- ("python-levenshtein" ,python-levenshtein)
- ("python-mappy" ,python-mappy)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-pysam" ,python-pysam)
- ("python-pyspoa" ,python-pyspoa)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)))
- (native-inputs
- `(("python-cython" ,python-cython)
- ("python-nose" ,python-nose)
- ("python-setuptools" ,python-setuptools)))
+ (list circtools
+ python-biopython
+ python-bwapy
+ python-levenshtein
+ python-mappy
+ python-numpy
+ python-pandas
+ python-pysam
+ python-pyspoa
+ python-scikit-learn
+ python-scipy))
+ (native-inputs
+ (list python-cython python-nose python-setuptools))
(home-page "https://ciri-cookbook.readthedocs.io/")
(synopsis "Circular RNA identification for Nanopore sequencing")
(description "CIRI-long is a package for circular RNA identification using
@@ -1583,14 +1541,14 @@ $(BOOST_LIB)/libboost_program_options.so"))))
(mkdir-p bin)
(install-file "bin/QTLtools" bin)))))))
(inputs
- `(("curl" ,curl)
- ("gsl" ,gsl)
- ("boost" ,boost)
- ("rmath-standalone" ,rmath-standalone)
- ("htslib" ,htslib-1.3)
- ("openssl" ,openssl)
- ("openblas" ,openblas)
- ("zlib" ,zlib)))
+ (list curl
+ gsl
+ boost
+ rmath-standalone
+ htslib-1.3
+ openssl
+ openblas
+ zlib))
(home-page "https://qtltools.github.io/qtltools/")
(synopsis "Tool set for molecular QTL discovery and analysis")
(description "QTLtools is a tool set for molecular QTL discovery
@@ -1653,8 +1611,7 @@ providing them a set of re-usable tools.")
;; so the tests fail.
#:out-of-source? #f))
(inputs
- `(("bpp-core" ,bpp-core)
- ("bpp-seq" ,bpp-seq)))
+ (list bpp-core bpp-seq))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "Bio++ phylogenetic Library")
(description
@@ -1685,8 +1642,7 @@ library provides phylogenetics-related modules.")
`(#:parallel-build? #f
#:tests? #f)) ; There are no tests.
(inputs
- `(("bpp-core" ,bpp-core)
- ("bpp-seq" ,bpp-seq)))
+ (list bpp-core bpp-seq))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "Bio++ population genetics library")
(description
@@ -1719,7 +1675,7 @@ library provides population genetics-related modules.")
;; so the tests fail.
#:out-of-source? #f))
(inputs
- `(("bpp-core" ,bpp-core)))
+ (list bpp-core))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "Bio++ sequence library")
(description
@@ -1750,9 +1706,7 @@ library provides sequence-related modules.")
`(#:parallel-build? #f
#:tests? #f)) ; There are no tests.
(native-inputs
- `(("groff" ,groff)
- ("man-db" ,man-db)
- ("texinfo" ,texinfo)))
+ (list groff man-db texinfo))
(inputs
`(("bpp-core" ,bpp-core)
("bpp-seq" ,bpp-seq)
@@ -1891,7 +1845,7 @@ package provides command line tools using the Bio++ library.")
("perl" ,perl)
("python" ,python-wrapper)))
(native-inputs
- `(("cpio" ,cpio)))
+ (list cpio))
(home-page "https://blast.ncbi.nlm.nih.gov")
(synopsis "Basic local alignment search tool")
(description
@@ -1977,13 +1931,9 @@ confidence to have in an alignment.")
'("bless" "kmc/bin/kmc")))))
(delete 'configure))))
(native-inputs
- `(("perl" ,perl)))
+ (list perl))
(inputs
- `(("openmpi" ,openmpi)
- ("boost" ,boost)
- ("sparsehash" ,sparsehash)
- ("pigz" ,pigz)
- ("zlib" ,zlib)))
+ (list openmpi boost sparsehash pigz zlib))
(supported-systems '("x86_64-linux"))
(home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
(synopsis "Bloom-filter-based error correction tool for NGS reads")
@@ -2042,10 +1992,7 @@ errors at the end of reads.")
("zlib" ,zlib)
("python" ,python-wrapper)))
(native-inputs
- `(("perl" ,perl)
- ("perl-clone" ,perl-clone)
- ("perl-test-deep" ,perl-test-deep)
- ("perl-test-simple" ,perl-test-simple)))
+ (list perl perl-clone perl-test-deep perl-test-simple))
(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
(synopsis "Fast and sensitive nucleotide sequence read aligner")
(description
@@ -2086,9 +2033,7 @@ gapped, local, and paired-end alignment modes.")
(modify-phases %standard-phases
(delete 'configure))))
(inputs
- `(("python-wrapper" ,python-wrapper)
- ("tbb" ,tbb-2020)
- ("zlib" ,zlib)))
+ (list python-wrapper tbb-2020 zlib))
(supported-systems '("x86_64-linux"))
(home-page "http://bowtie-bio.sourceforge.net/index.shtml")
(synopsis "Fast aligner for short nucleotide sequence reads")
@@ -2210,7 +2155,7 @@ splice junctions between exons.")
(install-file "bwa.1" man))))
;; no "configure" script
(delete 'configure))))
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(supported-systems '("x86_64-linux"))
@@ -2251,9 +2196,7 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
(substitute* "pssm.c"
(("inline int map") "int map"))))))))
(inputs
- `(("gdsl" ,gdsl)
- ("zlib" ,zlib)
- ("perl" ,perl)))
+ (list gdsl zlib perl))
(home-page "http://bwa-pssm.binf.ku.dk/")
(synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
(description
@@ -2292,9 +2235,9 @@ well as many of the command line options.")
(("^checkX.*") ""))
#t)))))
(inputs
- `(("bwa" ,bwa)))
+ (list bwa))
(native-inputs
- `(("python-toolshed" ,python-toolshed)))
+ (list python-toolshed))
(home-page "https://github.com/brentp/bwa-meth")
(synopsis "Fast and accurante alignment of BS-Seq reads")
(description
@@ -2322,13 +2265,11 @@ off-target reads for a capture method that targets CpG-rich region.")
"0mclahslz34vq9x424jmzsxk0nmpm1j716fa8h3zwr9ssvch7skc"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("python-lzo" ,python-lzo)
- ("python-nose" ,python-nose)
- ("python-cython" ,python-cython)))
+ (list python-lzo python-nose python-cython))
(home-page "https://github.com/bxlab/bx-python")
(synopsis "Tools for manipulating biological data")
(description
@@ -2350,13 +2291,9 @@ multiple sequence alignments.")
(arguments
`(#:tests? #f)) ; The tests require network access.
(native-inputs
- `(("python-psutil" ,python-psutil)
- ("python-htsget" ,python-htsget)))
+ (list python-psutil python-htsget))
(propagated-inputs
- `(("python-requests" ,python-requests)
- ("python-tqdm" ,python-tqdm)
- ("python-urllib3" ,python-urllib3)
- ("python-responses" ,python-responses)))
+ (list python-requests python-tqdm python-urllib3 python-responses))
(home-page "https://github.com/EGA-archive/ega-download-client")
(synopsis "Python client for EGA")
(description "This package is a python-based tool for viewing and
@@ -2428,18 +2365,16 @@ has several key features:
" and not TestHeaderCRAM"
" and not test_text_processing")))))))))
(propagated-inputs
- `(("htslib" ,htslib-1.10))) ; Included from installed header files.
+ (list htslib-1.10)) ; Included from installed header files.
(inputs
- `(("ncurses" ,ncurses)
- ("curl" ,curl)
- ("zlib" ,zlib)))
+ (list ncurses curl zlib))
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-pytest" ,python-pytest)
- ;; Dependencies below are are for tests only.
- ("samtools" ,samtools-1.10)
- ("bcftools" ,bcftools-1.10)
- ("python-nose" ,python-nose)))
+ (list python-cython
+ python-pytest
+ ;; Dependencies below are are for tests only.
+ samtools-1.10
+ bcftools-1.10
+ python-nose))
(home-page "https://github.com/pysam-developers/pysam")
(synopsis "Python bindings to the SAMtools C API")
(description
@@ -2468,7 +2403,7 @@ also includes an interface for tabix.")
;; Tests are not included
(arguments '(#:tests? #f))
(native-inputs
- `(("python-sphinx" ,python-sphinx)))
+ (list python-sphinx))
(home-page "https://github.com/benjschiller/twobitreader")
(synopsis "Python library for reading .2bit files")
(description
@@ -2491,17 +2426,16 @@ UCSC genome browser.")
;; Some test files are not included.
`(#:tests? #f))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)
- ("python-pandas" ,python-pandas)
- ("python-pysam" ,python-pysam)
- ("python-matplotlib" ,python-matplotlib)
- ("python-biopython" ,python-biopython)
- ("python-twobitreader" ,python-twobitreader)
- ("python-termcolor" ,python-termcolor)))
- (native-inputs
- `(("python-cython" ,python-cython)
- ("python-nose" ,python-nose)))
+ (list python-numpy
+ python-scipy
+ python-pandas
+ python-pysam
+ python-matplotlib
+ python-biopython
+ python-twobitreader
+ python-termcolor))
+ (native-inputs
+ (list python-cython python-nose))
(home-page "https://github.com/joshuagryphon/plastid")
(synopsis "Python library for genomic analysis")
(description
@@ -2558,12 +2492,12 @@ high-throughput sequencing data – with an emphasis on simplicity.")
"TEcount")))
#t)))))
(inputs
- `(("coreutils" ,coreutils)
- ("bedtools" ,bedtools)
- ("python-argparse" ,python2-argparse)
- ("python-pysam" ,python2-pysam)
- ("r-minimal" ,r-minimal)
- ("r-deseq2" ,r-deseq2)))
+ (list coreutils
+ bedtools
+ python2-argparse
+ python2-pysam
+ r-minimal
+ r-deseq2))
(home-page "https://github.com/mhammell-laboratory/tetoolkit")
(synopsis "Transposable elements in differential enrichment analysis")
(description
@@ -2615,7 +2549,7 @@ are not included due to their size.")
(mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(inputs
- `(("perl" ,perl)))
+ (list perl))
(home-page "http://weizhongli-lab.org/cd-hit/")
(synopsis "Cluster and compare protein or nucleotide sequences")
(description
@@ -2680,20 +2614,20 @@ setup"))))
;; This is not a library
(delete 'sanity-check))))
(inputs
- `(("htseq" ,htseq)
- ("python-pybedtools" ,python-pybedtools)
- ("python-cython" ,python-cython)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-matplotlib" ,python-matplotlib)
- ("python-pandas" ,python-pandas)
- ("python-pysam" ,python-pysam)
- ("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)))
- (native-inputs
- `(("python-setuptools-git" ,python-setuptools-git)
- ("python-mock" ,python-mock) ; for tests
- ("python-nose" ,python-nose) ; for tests
- ("python-pytz" ,python-pytz))) ; for tests
+ (list htseq
+ python-pybedtools
+ python-cython
+ python-scikit-learn
+ python-matplotlib
+ python-pandas
+ python-pysam
+ python-numpy
+ python-scipy))
+ (native-inputs
+ (list python-setuptools-git
+ python-mock ; for tests
+ python-nose ; for tests
+ python-pytz)) ; for tests
(home-page "https://github.com/YeoLab/clipper")
(synopsis "CLIP peak enrichment recognition")
(description
@@ -2729,7 +2663,7 @@ setup"))))
(install-file "CodingQuarry" bin)
(install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))
#t)))))
- (inputs `(("openmpi" ,openmpi)))
+ (inputs (list openmpi))
(native-search-paths
(list (search-path-specification
(variable "QUARRY_PATH")
@@ -2754,7 +2688,7 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
"1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
(build-system gnu-build-system)
(inputs
- `(("argtable" ,argtable)))
+ (list argtable))
(home-page "http://www.clustal.org/omega/")
(synopsis "Multiple sequence aligner for protein and DNA/RNA")
(description
@@ -2782,14 +2716,10 @@ time.")
(delete-file-recursively ".eggs")))))
(build-system python-build-system)
(inputs
- `(("python-bx-python" ,python-bx-python)
- ("python-numpy" ,python-numpy)
- ("python-pybigwig" ,python-pybigwig)
- ("python-pysam" ,python-pysam)
- ("zlib" ,zlib)))
+ (list python-bx-python python-numpy python-pybigwig python-pysam
+ zlib))
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-nose" ,python-nose)))
+ (list python-cython python-nose))
(home-page "http://crossmap.sourceforge.net/")
(synopsis "Convert genome coordinates between assemblies")
(description
@@ -2811,9 +2741,7 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
"14v5yyasq2bz34j38wi3xfcp06jj7l35ppibjcn95l2n73hz3zwi"))))
(build-system python-build-system)
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-pytest" ,python-pytest)
- ("python-xopen" ,python-xopen)))
+ (list python-cython python-pytest python-xopen))
(home-page "https://github.com/marcelm/dnaio/")
(synopsis "Read FASTA and FASTQ files efficiently")
(description
@@ -2833,7 +2761,7 @@ files. The code was previously part of the cutadapt tool.")
"1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x"))))
(build-system python-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/deeptools/deeptools_intervals")
(synopsis "Create GTF-based interval trees with associated meta-data")
(description
@@ -2857,18 +2785,17 @@ interval trees with associated meta-data. It is primarily used by the
"0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl"))))
(build-system python-build-system)
(native-inputs
- `(("python-mock" ,python-mock)
- ("python-nose" ,python-nose)))
+ (list python-mock python-nose))
(propagated-inputs
- `(("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)
- ("python-numpydoc" ,python-numpydoc)
- ("python-py2bit" ,python-py2bit)
- ("python-pybigwig" ,python-pybigwig)
- ("python-pysam" ,python-pysam)
- ("python-scipy" ,python-scipy)
- ("python-deeptoolsintervals" ,python-deeptoolsintervals)
- ("python-plotly" ,python-plotly-2.4.1)))
+ (list python-matplotlib
+ python-numpy
+ python-numpydoc
+ python-py2bit
+ python-pybigwig
+ python-pysam
+ python-scipy
+ python-deeptoolsintervals
+ python-plotly-2.4.1))
(home-page "https://pypi.org/project/deepTools/")
(synopsis "Useful tools for exploring deep sequencing data")
(description "This package addresses the challenge of handling large amounts
@@ -2907,12 +2834,9 @@ annotations of the genome.")
(("os.path.exists\\('PKG-INFO'\\):")
"os.path.exists('totally-does-not-exist'):")))))))
(inputs
- `(("python-dnaio" ,python-dnaio)
- ("python-xopen" ,python-xopen)))
+ (list python-dnaio python-xopen))
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-pytest" ,python-pytest)
- ("python-setuptools-scm" ,python-setuptools-scm)))
+ (list python-cython python-pytest python-setuptools-scm))
(home-page "https://cutadapt.readthedocs.io/en/stable/")
(synopsis "Remove adapter sequences from nucleotide sequencing reads")
(description
@@ -2944,8 +2868,7 @@ other types of unwanted sequence from high-throughput sequencing reads.")
(modify-phases %standard-phases
(delete 'configure))))
(inputs
- `(("zlib" ,zlib)
- ("curl" ,curl)))
+ (list zlib curl))
(native-inputs
`(("doxygen" ,doxygen)
;; Need for tests
@@ -2983,11 +2906,9 @@ files.")
(("libs=\\[") "libs=[\"BigWig\", "))
#t)))))
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(inputs
- `(("libbigwig" ,libbigwig)
- ("zlib" ,zlib)
- ("curl" ,curl)))
+ (list libbigwig zlib curl))
(home-page "https://github.com/dpryan79/pyBigWig")
(synopsis "Access bigWig files in Python using libBigWig")
(description
@@ -3022,18 +2943,16 @@ accessing bigWig files.")
"\"test requires network access\")\n"
all))))))))
(propagated-inputs
- `(("python-cachecontrol" ,python-cachecontrol)
- ("python-lockfile" ,python-lockfile)
- ("python-mistune" ,python-mistune)
- ("python-rdflib" ,python-rdflib)
- ("python-rdflib-jsonld" ,python-rdflib-jsonld)
- ("python-requests" ,python-requests)
- ("python-ruamel.yaml" ,python-ruamel.yaml)
- ("python-typing-extensions" ,python-typing-extensions)))
- (native-inputs
- `(("python-black" ,python-black)
- ("python-pytest" ,python-pytest)
- ("python-pytest-runner" ,python-pytest-runner)))
+ (list python-cachecontrol
+ python-lockfile
+ python-mistune
+ python-rdflib
+ python-rdflib-jsonld
+ python-requests
+ python-ruamel.yaml
+ python-typing-extensions))
+ (native-inputs
+ (list python-black python-pytest python-pytest-runner))
(home-page "https://github.com/common-workflow-language/schema_salad")
(synopsis "Schema Annotations for Linked Avro Data (SALAD)")
(description
@@ -3105,30 +3024,30 @@ and record oriented data modeling and the Semantic Web.")
(substitute* "tox.ini"
(("-n auto") "")))))))
(propagated-inputs
- `(("python-argcomplete" ,python-argcomplete)
- ("python-bagit" ,python-bagit)
- ("python-coloredlogs" ,python-coloredlogs)
- ("python-mypy-extensions" ,python-mypy-extensions)
- ("python-prov" ,python-prov)
- ("python-pydot" ,python-pydot)
- ("python-psutil" ,python-psutil)
- ("python-rdflib" ,python-rdflib)
- ("python-requests" ,python-requests)
- ("python-ruamel.yaml" ,python-ruamel.yaml)
- ("python-schema-salad" ,python-schema-salad)
- ("python-shellescape" ,python-shellescape)
- ("python-typing-extensions" ,python-typing-extensions)
- ;; Not listed as needed but still necessary:
- ("node" ,node)))
- (native-inputs
- `(("python-arcp" ,python-arcp)
- ("python-humanfriendly" ,python-humanfriendly)
- ("python-mock" ,python-mock)
- ("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-pytest-mock" ,python-pytest-mock)
- ("python-pytest-runner" ,python-pytest-runner)
- ("python-rdflib-jsonld" ,python-rdflib-jsonld)))
+ (list python-argcomplete
+ python-bagit
+ python-coloredlogs
+ python-mypy-extensions
+ python-prov
+ python-pydot
+ python-psutil
+ python-rdflib
+ python-requests
+ python-ruamel.yaml
+ python-schema-salad
+ python-shellescape
+ python-typing-extensions
+ ;; Not listed as needed but still necessary:
+ node))
+ (native-inputs
+ (list python-arcp
+ python-humanfriendly
+ python-mock
+ python-pytest
+ python-pytest-cov
+ python-pytest-mock
+ python-pytest-runner
+ python-rdflib-jsonld))
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis "Common Workflow Language reference implementation")
@@ -3257,10 +3176,7 @@ with Python.")
(copy-recursively "excludeTemplates" templates)
#t))))))
(inputs
- `(("boost" ,boost)
- ("bzip2" ,bzip2)
- ("htslib" ,htslib)
- ("zlib" ,zlib)))
+ (list boost bzip2 htslib zlib))
(home-page "https://github.com/dellytools/delly")
(synopsis "Integrated structural variant prediction method")
(description "Delly is an integrated structural variant prediction method
@@ -3333,12 +3249,12 @@ bases are detected.")
(wrap-program (string-append bin "/RepeatMasker")
`("PERL5LIB" ":" prefix (,path ,share)))))))))
(inputs
- `(("perl" ,perl)
- ("perl-text-soundex" ,perl-text-soundex)
- ("python" ,python)
- ("python-h5py" ,python-h5py)
- ("hmmer" ,hmmer)
- ("trf" ,trf)))
+ (list perl
+ perl-text-soundex
+ python
+ python-h5py
+ hmmer
+ trf))
(home-page "https://github.com/Benson-Genomics-Lab/TRF")
(synopsis "Tandem Repeats Finder: a program to analyze DNA sequences")
(description "A tandem repeat in DNA is two or more adjacent, approximate
@@ -3373,7 +3289,7 @@ bases are detected.")
(substitute* "CMakeLists.txt" (("-march=native") ""))
#t)))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/bbuchfink/diamond")
(synopsis "Accelerated BLAST compatible local sequence aligner")
(description
@@ -3428,9 +3344,7 @@ data and settings.")
(("#define FASTA_HPP" line)
(string-append line "\n#include <random>"))))))))
(inputs
- `(("boost" ,boost)
- ("cairo" ,cairo)
- ("rmath-standalone" ,rmath-standalone)))
+ (list boost cairo rmath-standalone))
(native-inputs
`(("texlive" ,(texlive-updmap.cfg (list texlive-cm
texlive-amsfonts
@@ -3491,11 +3405,8 @@ of nucleic acid binding proteins.")
(find-files "../bin" ".*"))
#t))))))
(inputs
- `(("gsl" ,gsl)
- ("lapack" ,lapack)
- ("openblas" ,openblas)
- ("perl" ,perl)
- ("gfortran" ,gfortran "lib")))
+ (list gsl lapack openblas perl
+ `(,gfortran "lib")))
(home-page "https://github.com/DReichLab/EIG")
(synopsis "Tools for population genetics")
(description "The EIGENSOFT package provides tools for population
@@ -3585,23 +3496,23 @@ quantitative phenotypes.")
"-filter" "-help")
#t)))))
(inputs
- `(("edirect-go-programs" ,edirect-go-programs)
- ("perl-html-parser" ,perl-html-parser)
- ("perl-encode-locale" ,perl-encode-locale)
- ("perl-file-listing" ,perl-file-listing)
- ("perl-html-tagset" ,perl-html-tagset)
- ("perl-html-tree" ,perl-html-tree)
- ("perl-http-cookies" ,perl-http-cookies)
- ("perl-http-date" ,perl-http-date)
- ("perl-http-message" ,perl-http-message)
- ("perl-http-negotiate" ,perl-http-negotiate)
- ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
- ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
- ("perl-net-http" ,perl-net-http)
- ("perl-uri" ,perl-uri)
- ("perl-www-robotrules" ,perl-www-robotrules)
- ("perl-xml-simple" ,perl-xml-simple)
- ("perl" ,perl)))
+ (list edirect-go-programs
+ perl-html-parser
+ perl-encode-locale
+ perl-file-listing
+ perl-html-tagset
+ perl-html-tree
+ perl-http-cookies
+ perl-http-date
+ perl-http-message
+ perl-http-negotiate
+ perl-lwp-mediatypes
+ perl-lwp-protocol-https
+ perl-net-http
+ perl-uri
+ perl-www-robotrules
+ perl-xml-simple
+ perl))
(home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/")
(synopsis "Tools for accessing the NCBI's set of databases")
(description
@@ -3658,16 +3569,16 @@ software to answer ad hoc questions.")
(native-inputs '())
(propagated-inputs '())
(inputs
- `(("go-github-com-fatih-color" ,go-github-com-fatih-color)
- ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg)
- ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector)
- ("go-github-com-golang-freetype" ,go-github-com-golang-freetype)
- ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid)
- ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory)
- ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2)
- ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode)
- ("go-golang-org-x-image" ,go-golang-org-x-image)
- ("go-golang-org-x-text" ,go-golang-org-x-text)))))
+ (list go-github-com-fatih-color
+ go-github-com-fogleman-gg
+ go-github-com-gedex-inflector
+ go-github-com-golang-freetype
+ go-github-com-klauspost-cpuid
+ go-github-com-pbnjay-memory
+ go-github-com-surgebase-porter2
+ go-golang-org-rainycape-unidecode
+ go-golang-org-x-image
+ go-golang-org-x-text))))
(define-public exonerate
(package
@@ -3687,9 +3598,9 @@ software to answer ad hoc questions.")
(arguments
`(#:parallel-build? #f)) ; Building in parallel fails on some machines.
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(inputs
- `(("glib" ,glib)))
+ (list glib))
(home-page
"https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
(synopsis "Generic tool for biological sequence alignment")
@@ -3736,10 +3647,7 @@ dynamic programming or a variety of heuristics.")
(("check_version\\(PACKAGE_VERSION\\);") ""))
#t)))))
(inputs
- `(("boost" ,boost)
- ("bamtools" ,bamtools)
- ("protobuf" ,protobuf)
- ("zlib" ,zlib)))
+ (list boost bamtools protobuf zlib))
(home-page "http://bio.math.berkeley.edu/eXpress")
(synopsis "Streaming quantification for high-throughput genomic sequencing")
(description
@@ -3859,10 +3767,10 @@ reasonable amount of time and memory. For large alignments, FastTree is
"01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
(build-system gnu-build-system)
(inputs
- `(("libgtextutils" ,libgtextutils)))
+ (list libgtextutils))
(native-inputs
- `(("gcc" ,gcc-6) ;; doesn't build with later versions
- ("pkg-config" ,pkg-config)))
+ (list gcc-6 ;; doesn't build with later versions
+ pkg-config))
(home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
(synopsis "Tools for FASTA/FASTQ file preprocessing")
(description
@@ -3909,11 +3817,9 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(bin (string-append out "/bin/")))
(install-file "flexbar" bin)))))))
(inputs
- `(("tbb" ,tbb-2020)
- ("zlib" ,zlib)))
+ (list tbb-2020 zlib))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("seqan" ,seqan-2)))
+ (list pkg-config seqan-2))
(home-page "https://github.com/seqan/flexbar")
(synopsis "Barcode and adapter removal tool for sequencing platforms")
(description
@@ -4052,8 +3958,7 @@ genes in incomplete assemblies or complete genomes.")
(install-file "fxtract" bin)
#t))))))
(inputs
- `(("pcre" ,pcre)
- ("zlib" ,zlib)))
+ (list pcre zlib))
(native-inputs
;; ctskennerton-util is licensed under GPL2.
`(("ctskennerton-util"
@@ -4100,9 +4005,7 @@ comment or quality sections.")
#t))))
(build-system gnu-build-system)
(inputs
- `(("gsl" ,gsl)
- ("openblas" ,openblas)
- ("zlib" ,zlib)))
+ (list gsl openblas zlib))
(native-inputs
`(("catch" ,catch-framework2-1)
("perl" ,perl)
@@ -4166,12 +4069,9 @@ genome-wide association studies}.")
(("Cython.Setup") "Cython.Build"))
#t)))))
(inputs
- `(("python-scipy" ,python2-scipy)
- ("python-numpy" ,python2-numpy)
- ("python-pysam" ,python2-pysam)
- ("python-networkx" ,python2-networkx)))
+ (list python2-scipy python2-numpy python2-pysam python2-networkx))
(native-inputs
- `(("python-cython" ,python2-cython)))
+ (list python2-cython))
;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21.
(home-page "https://github.com/nboley/grit")
(synopsis "Tool for integrative analysis of RNA-seq type assays")
@@ -4234,11 +4134,9 @@ estimates transcript expression.")
"hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))))
(delete 'configure))))
(native-inputs
- `(("unzip" ,unzip)))
+ (list unzip))
(inputs
- `(("perl" ,perl)
- ("python" ,python)
- ("zlib" ,zlib)))
+ (list perl python zlib))
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(supported-systems '("x86_64-linux"))
@@ -4297,8 +4195,7 @@ particular, reads spanning multiple exons.")
(mkdir-p doc)
(install-file "doc/manual.inc.html" doc)))))))
(native-inputs
- `(("perl" ,perl)
- ("pandoc" ,pandoc))) ; for documentation
+ (list perl pandoc)) ; for documentation
(inputs
`(("python" ,python-wrapper)))
(home-page "https://daehwankimlab.github.io/hisat2/")
@@ -4329,8 +4226,7 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
(base32
"0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj"))))
(build-system gnu-build-system)
- (native-inputs `(("perl" ,perl)
- ("python" ,python))) ; for tests
+ (native-inputs (list perl python)) ; for tests
(home-page "http://hmmer.org/")
(synopsis "Biosequence analysis using profile hidden Markov models")
(description
@@ -4355,13 +4251,12 @@ HMMs).")
"0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b"))))
(build-system python-build-system)
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
;; Numpy needs to be propagated when htseq is used as a Python library.
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(inputs
- `(("python-pysam" ,python-pysam)
- ("python-matplotlib" ,python-matplotlib)))
+ (list python-pysam python-matplotlib))
(home-page "https://htseq.readthedocs.io/")
(synopsis "Analysing high-throughput sequencing data with Python")
(description
@@ -4411,7 +4306,7 @@ from high-throughput sequencing assays.")
("java-commons-jexl-2" ,java-commons-jexl-2)
("java-xz" ,java-xz)))
(native-inputs
- `(("java-testng" ,java-testng)))
+ (list java-testng))
(home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
@@ -4454,7 +4349,7 @@ manipulating HTS data.")
("java-commons-jexl-2" ,java-commons-jexl-2)
("java-xz" ,java-xz)))
(native-inputs
- `(("java-junit" ,java-junit)))
+ (list java-junit))
(home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
@@ -4557,10 +4452,9 @@ manipulating HTS data.")
#t))
(replace 'install (install-jars "dist")))))
(inputs
- `(("java-htsjdk" ,java-htsjdk)
- ("java-guava" ,java-guava)))
+ (list java-htsjdk java-guava))
(native-inputs
- `(("java-testng" ,java-testng)))
+ (list java-testng))
(home-page "http://broadinstitute.github.io/picard/")
(synopsis "Tools for manipulating high-throughput sequencing data and formats")
(description "Picard is a set of Java command line tools for manipulating
@@ -4647,10 +4541,9 @@ Class-Path: /~a \
(rename-file "build.xml.new" "build.xml")
#t)))))
(propagated-inputs
- `(("java-htsjdk" ,java-htsjdk-2.10.1)))
+ (list java-htsjdk-2.10.1))
(native-inputs
- `(("java-testng" ,java-testng)
- ("java-guava" ,java-guava)))
+ (list java-testng java-guava))
(home-page "http://broadinstitute.github.io/picard/")
(synopsis "Tools for manipulating high-throughput sequencing data and formats")
(description "Picard is a set of Java command line tools for manipulating
@@ -4831,7 +4724,7 @@ VCF.")
("java-picard-1.113" ,java-picard-1.113)
("java-jbzip2" ,java-jbzip2)))
(native-inputs
- `(("unzip" ,unzip)))
+ (list unzip))
(home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
(synopsis "Quality control tool for high throughput sequence data")
(description
@@ -4880,7 +4773,7 @@ The main functions of FastQC are:
(lambda* (#:key outputs #:allow-other-keys)
(mkdir-p (string-append (assoc-ref outputs "out") "/bin")))))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/OpenGene/fastp/")
(synopsis "All-in-one FastQ preprocessor")
(description
@@ -4910,13 +4803,12 @@ performance.")
"--enable-libcurl"
"--enable-s3")))
(inputs
- `(("curl" ,curl)
- ("openssl" ,openssl)))
+ (list curl openssl))
;; This is referred to in the pkg-config file as a required library.
(propagated-inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("perl" ,perl)))
+ (list perl))
(home-page "https://www.htslib.org")
(synopsis "C library for reading/writing high-throughput sequencing data")
(description
@@ -5013,12 +4905,9 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and
;; causes the tests to always fail.
(arguments `(#:tests? #f))
(propagated-inputs
- `(("python-scipy" ,python-scipy)
- ("python-sympy" ,python-sympy)
- ("python-numpy" ,python-numpy)
- ("python-matplotlib" ,python-matplotlib)))
+ (list python-scipy python-sympy python-numpy python-matplotlib))
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
(home-page "https://github.com/nboley/idr")
(synopsis "Tool to measure the irreproducible discovery rate (IDR)")
(description
@@ -5059,7 +4948,7 @@ experiments and provide highly stable thresholds based on reproducibility.")
("python" ,python-wrapper)
("pkg-config" ,pkg-config)))
(inputs
- `(("htslib" ,htslib)))
+ (list htslib))
(synopsis "Tool for fast counting of k-mers in DNA")
(description
"Jellyfish is a tool for fast, memory-efficient counting of k-mers in
@@ -5140,15 +5029,9 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
(add-installed-pythonpath inputs outputs)
(invoke "pytest" "-v")))))))
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-pytest" ,python-pytest)
- ("python-pytest-runner" ,python-pytest-runner)))
+ (list python-cython python-pytest python-pytest-runner))
(inputs
- `(("zlib" ,zlib)
- ("bzip2" ,bzip2)
- ("seqan" ,seqan-1)
- ("python-screed" ,python-screed)
- ("python-bz2file" ,python-bz2file)))
+ (list zlib bzip2 seqan-1 python-screed python-bz2file))
(home-page "https://khmer.readthedocs.org/")
(synopsis "K-mer counting, filtering and graph traversal library")
(description "The khmer software is a set of command-line tools for
@@ -5190,8 +5073,7 @@ data.")
(copy-recursively "bin" bin))
#t)))))
(inputs
- `(("perl" ,perl)
- ("zlib" ,zlib)))
+ (list perl zlib))
(home-page "http://kaiju.binf.ku.dk/")
(synopsis "Fast and sensitive taxonomic classification for metagenomics")
(description "Kaiju is a program for sensitive taxonomic classification
@@ -5236,10 +5118,9 @@ experiments.")
(add-installed-pythonpath inputs outputs)
(invoke "pytest" "-v")))))))
(inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-pytest" ,python-pytest)))
+ (list python-cython python-pytest))
(home-page "https://github.com/macs3-project/MACS")
(synopsis "Model based analysis for ChIP-Seq data")
(description
@@ -5319,11 +5200,7 @@ sequencing tag position and orientation.")
`("PATH" ":" prefix (,path))))
(find-files bin))))))))
(inputs
- `(("perl" ,perl)
- ("ruby" ,ruby)
- ("gawk" ,gawk)
- ("grep" ,grep)
- ("coreutils" ,coreutils)))
+ (list perl ruby gawk grep coreutils))
(home-page "https://mafft.cbrc.jp/alignment/software/")
(synopsis "Multiple sequence alignment program")
(description
@@ -5380,14 +5257,14 @@ sequences).")
(("c\\+\\+11") "c++14"))
#t)))))
(native-inputs
- `(("autoconf" ,autoconf)))
+ (list autoconf))
(inputs
- `(;; Capnproto and htslib are statically embedded in the final
- ;; application. Therefore we also list their licenses, below.
- ("capnproto" ,capnproto)
- ("htslib" ,htslib)
- ("gsl" ,gsl)
- ("zlib" ,zlib)))
+ (list ;; Capnproto and htslib are statically embedded in the final
+ ;; application. Therefore we also list their licenses, below.
+ capnproto
+ htslib
+ gsl
+ zlib))
(supported-systems '("x86_64-linux"))
(home-page "https://mash.readthedocs.io")
(synopsis "Fast genome and metagenome distance estimation using MinHash")
@@ -5439,11 +5316,7 @@ form of assemblies or reads.")
(("set\\(Boost.*") "")
(("add_dependencies.*") "")))))))
(inputs
- `(("zlib" ,zlib)
- ("perl" ,perl)
- ("samtools" ,samtools)
- ("htslib" ,htslib)
- ("boost" ,boost)))
+ (list zlib perl samtools htslib boost))
(home-page "https://bitbucket.org/berkeleylab/metabat")
(synopsis
"Reconstruction of single genomes from complex microbial communities")
@@ -5547,14 +5420,11 @@ linker_so='gcc -shared'); defines")))))
(inputs
;; Samtools must not be newer than 1.2. See
;; https://github.com/yarden/MISO/issues/135
- `(("samtools" ,samtools-1.2)
- ("python-numpy" ,python2-numpy)
- ("python-pysam" ,python2-pysam)
- ("python-scipy" ,python2-scipy)
- ("python-matplotlib" ,python2-matplotlib)))
+ (list samtools-1.2 python2-numpy python2-pysam python2-scipy
+ python2-matplotlib))
(native-inputs
- `(("python-mock" ,python2-mock) ; for tests
- ("python-pytz" ,python2-pytz))) ; for tests
+ (list python2-mock ; for tests
+ python2-pytz)) ; for tests
(home-page "https://miso.readthedocs.io/en/fastmiso/")
(synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
(description
@@ -5622,13 +5492,9 @@ program for nucleotide and protein sequences.")
(inputs
;; XXX: TODO: Enable Lua and Guile bindings.
;; https://github.com/tjunier/newick_utils/issues/13
- `(("libxml2" ,libxml2)
- ("flex" ,flex)
- ("bison" ,bison)))
+ (list libxml2 flex bison))
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("libtool" ,libtool)))
+ (list autoconf automake libtool))
(synopsis "Programs for working with newick format phylogenetic trees")
(description
"Newick-utils is a suite of utilities for processing phylogenetic trees
@@ -5650,11 +5516,9 @@ trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
(base32
"16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
(build-system gnu-build-system)
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
(native-inputs
- `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
- ("ruby-rspec" ,ruby-rspec)
- ("ruby" ,ruby)))
+ (list ruby-bio-commandeer ruby-rspec ruby))
(synopsis "Simple and not slow open reading frame (ORF) caller")
(description
"An ORF caller finds stretches of DNA that, when translated, are not
@@ -5685,13 +5549,9 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
(("^sphinx") ""))
#t)))))
(propagated-inputs
- `(("python-cython" ,python2-cython)
- ("python-numpy" ,python2-numpy)
- ("python-pysam" ,python2-pysam)
- ("python-h5py" ,python2-h5py)))
+ (list python2-cython python2-numpy python2-pysam python2-h5py))
(native-inputs
- `(("python-nose" ,python2-nose)
- ("python-pyxb" ,python2-pyxb)))
+ (list python2-nose python2-pyxb))
(home-page "https://pacificbiosciences.github.io/pbcore/")
(synopsis "Library for reading and writing PacBio data files")
(description
@@ -5723,17 +5583,15 @@ files and writing bioinformatics applications.")
"from scipy import linalg\nimport weave"))
#t)))))
(propagated-inputs
- `(("python-scipy" ,python2-scipy)
- ("python-numpy" ,python2-numpy)
- ("python-matplotlib" ,python2-matplotlib)
- ("python-fastlmm" ,python2-fastlmm)
- ("python-pandas" ,python2-pandas)
- ("python-pysnptools" ,python2-pysnptools)
- ("python-weave" ,python2-weave)))
- (native-inputs
- `(("python-mock" ,python2-mock)
- ("python-nose" ,python2-nose)
- ("unzip" ,unzip)))
+ (list python2-scipy
+ python2-numpy
+ python2-matplotlib
+ python2-fastlmm
+ python2-pandas
+ python2-pysnptools
+ python2-weave))
+ (native-inputs
+ (list python2-mock python2-nose unzip))
(home-page "https://github.com/PMBio/warpedLMM")
(synopsis "Implementation of warped linear mixed models")
(description
@@ -5781,9 +5639,7 @@ the phenotype as it models the data.")
`("PATH" ":" prefix (,path)))
(install-file "prank.1" man)))))))
(inputs
- `(("mafft" ,mafft)
- ("exonerate" ,exonerate)
- ("bppsuite" ,bppsuite)))
+ (list mafft exonerate bppsuite))
(home-page "http://wasabiapp.org/software/prank/")
(synopsis "Probabilistic multiple sequence alignment program")
(description
@@ -5855,7 +5711,7 @@ predicts the locations of structural units in the sequences.")
("lapack" ,lapack)
("openblas" ,openblas)))
(native-inputs
- `(("which" ,which)))
+ (list which))
(home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
(synopsis "Detect orthologous genes across species")
(description
@@ -5884,7 +5740,7 @@ large-scale data and can be applied to hundreds of species at once.")
`(#:python ,python-2 ; does not work with Python 3
#:tests? #f)) ; there are no tests
(inputs
- `(("python2-matplotlib" ,python2-matplotlib)))
+ (list python2-matplotlib))
(home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
(synopsis "Analyze high-throughput genetic sequencing data")
(description
@@ -6008,10 +5864,7 @@ partial genes, and identifies translation initiation sites.")
(,(string-append coreutils-path ":" out "/bin"))))))
#t)))))
(native-inputs
- `(("perl-env-path" ,perl-env-path)
- ("perl-test-files" ,perl-test-files)
- ("perl-test-most" ,perl-test-most)
- ("perl-test-output" ,perl-test-output)))
+ (list perl-env-path perl-test-files perl-test-most perl-test-output))
(inputs
`(("perl-array-utils" ,perl-array-utils)
("bioperl" ,bioperl-minimal)
@@ -6084,7 +5937,7 @@ extremely diverse sets of genomes.")
(symlink (string-append bin "/" executable) "raxml"))
#t)))))
(inputs
- `(("openmpi" ,openmpi)))
+ (list openmpi))
(home-page "https://cme.h-its.org/exelixis/web/software/raxml/index.html")
(synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
(description
@@ -6172,11 +6025,7 @@ phylogenies.")
"rsem-run-ebseq"
"rsem-run-prsem-testing-procedure"))))))))
(inputs
- `(("boost" ,boost)
- ("r-minimal" ,r-minimal)
- ("perl" ,perl)
- ("htslib" ,htslib-1.3)
- ("zlib" ,zlib)))
+ (list boost r-minimal perl htslib-1.3 zlib))
(home-page "http://deweylab.biostat.wisc.edu/rsem/")
(synopsis "Estimate gene expression levels from RNA-Seq data")
(description
@@ -6204,14 +6053,14 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
"0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m"))))
(build-system python-build-system)
(inputs
- `(("python-cython" ,python-cython)
- ("python-bx-python" ,python-bx-python)
- ("python-pybigwig" ,python-pybigwig)
- ("python-pysam" ,python-pysam)
- ("python-numpy" ,python-numpy)
- ("zlib" ,zlib)))
+ (list python-cython
+ python-bx-python
+ python-pybigwig
+ python-pysam
+ python-numpy
+ zlib))
(native-inputs
- `(("python-nose" ,python-nose)))
+ (list python-nose))
(home-page "http://rseqc.sourceforge.net/")
(synopsis "RNA-seq quality control package")
(description
@@ -6271,7 +6120,7 @@ distribution, coverage uniformity, strand specificity, etc.")
("python" ,python)
("readline" ,readline)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "http://seek.princeton.edu")
(synopsis "Gene co-expression search engine")
(description
@@ -6329,13 +6178,9 @@ to the user's query of interest.")
(install-file file include))
(scandir "." (lambda (name) (string-match "\\.h$" name))))
#t))))))
- (native-inputs `(("pkg-config" ,pkg-config)))
+ (native-inputs (list pkg-config))
(inputs
- `(("htslib" ,htslib)
- ("ncurses" ,ncurses)
- ("perl" ,perl)
- ("python" ,python)
- ("zlib" ,zlib)))
+ (list htslib ncurses perl python zlib))
(home-page "http://samtools.sourceforge.net")
(synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
(description
@@ -6364,11 +6209,7 @@ viewer.")
(delete-file-recursively "htslib-1.10")
#t))))
(inputs
- `(("htslib" ,htslib-1.10)
- ("ncurses" ,ncurses)
- ("perl" ,perl)
- ("python" ,python)
- ("zlib" ,zlib)))))
+ (list htslib-1.10 ncurses perl python zlib))))
(define-public samtools-1.2
(package (inherit samtools)
@@ -6423,15 +6264,9 @@ viewer.")
(("P 52.out.*") ""))))
(delete 'configure))))
(native-inputs
- `(("grep" ,grep)
- ("gawk" ,gawk)
- ("pkg-config" ,pkg-config)))
+ (list grep gawk pkg-config))
(inputs
- `(("htslib" ,htslib-for-samtools-1.2)
- ("ncurses" ,ncurses)
- ("perl" ,perl)
- ("python" ,python)
- ("zlib" ,zlib)))))
+ (list htslib-for-samtools-1.2 ncurses perl python zlib))))
(define-public samtools-0.1
;; This is the most recent version of the 0.1 line of samtools. The input
@@ -6543,8 +6378,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
(mkdir-p share)
(copy-recursively "../R" share)))))))
(inputs
- `(("boost" ,boost)
- ("htslib" ,htslib)))
+ (list boost htslib))
(home-page "https://github.com/friendsofstrandseq/mosaicatcher")
(synopsis "Count and classify Strand-seq reads")
(description
@@ -6586,7 +6420,7 @@ each chromosome in each cell using a Hidden Markov Model.")
#t)))
(add-after 'unpack 'enter-dir
(lambda _ (chdir "ngs-sdk") #t)))))
- (native-inputs `(("perl" ,perl)))
+ (native-inputs (list perl))
;; According to the test
;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
;; in ngs-sdk/setup/konfigure.perl
@@ -6724,7 +6558,7 @@ simultaneously.")
("java-ngs" ,java-ngs)
("libmagic" ,file)
("hdf5" ,hdf5)))
- (native-inputs `(("perl" ,perl)))
+ (native-inputs (list perl))
;; NCBI-VDB requires SSE capability.
(supported-systems '("i686-linux" "x86_64-linux"))
(home-page "https://github.com/ncbi/ncbi-vdb")
@@ -6770,10 +6604,9 @@ accessed/downloaded on demand across HTTP.")
"/bin/")))
(install-file "plink" bin)))))))
(inputs
- `(("zlib" ,zlib)
- ("lapack" ,lapack)))
+ (list zlib lapack))
(native-inputs
- `(("unzip" ,unzip)))
+ (list unzip))
(home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
(synopsis "Whole genome association analysis toolset")
(description
@@ -6830,13 +6663,9 @@ subsequent visualization, annotation and storage of results.")
(invoke "bash" "test_setup.sh")
(invoke "python3" "tests.py"))))))))
(inputs
- `(("lapack" ,lapack)
- ("openblas" ,openblas)
- ("zlib" ,zlib)))
+ (list lapack openblas zlib))
(native-inputs
- `(("diffutils" ,diffutils)
- ("plink" ,plink)
- ("python" ,python))) ; for tests
+ (list diffutils plink python)) ; for tests
(home-page "https://www.cog-genomics.org/plink/")
(license license:gpl3+)))
@@ -6883,8 +6712,7 @@ subsequent visualization, annotation and storage of results.")
#t))
(delete 'configure))))
(inputs
- `(("samtools" ,samtools-0.1)
- ("zlib" ,zlib)))
+ (list samtools-0.1 zlib))
(home-page "https://github.com/smithlabcode/smithlab_cpp")
(synopsis "C++ helper library for functions used in Smith lab projects")
(description
@@ -6924,10 +6752,7 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
"PROGS=preseq"
"INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
(inputs
- `(("gsl" ,gsl)
- ("samtools" ,samtools-0.1)
- ("smithlab-cpp" ,smithlab-cpp)
- ("zlib" ,zlib)))
+ (list gsl samtools-0.1 smithlab-cpp zlib))
(home-page "http://smithlabresearch.org/software/preseq/")
(synopsis "Program for analyzing library complexity")
(description
@@ -6953,11 +6778,9 @@ complexity samples.")
"148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx"))))
(build-system python-build-system)
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-pytest-runner" ,python-pytest-runner)))
+ (list python-pytest python-pytest-cov python-pytest-runner))
(inputs
- `(("python-bz2file" ,python-bz2file)))
+ (list python-bz2file))
(home-page "https://github.com/dib-lab/screed/")
(synopsis "Short read sequence database utilities")
(description "Screed parses FASTA and FASTQ files and generates databases.
@@ -7055,7 +6878,7 @@ sequence itself can be retrieved from these databases.")
(string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5")))
#t)))))
- (native-inputs `(("perl" ,perl)))
+ (native-inputs (list perl))
(inputs
`(("ngs-sdk" ,ngs-sdk)
("ncbi-vdb" ,ncbi-vdb)
@@ -7093,9 +6916,7 @@ writing files into the .sra format.")
(lambda _
(invoke "ctest" "test" "--output-on-failure"))))))
(native-inputs
- `(("bzip2" ,bzip2)
- ("cereal" ,cereal)
- ("zlib" ,zlib)))
+ (list bzip2 cereal zlib))
(home-page "https://www.seqan.de")
(synopsis "Library for nucleotide sequence analysis")
(description
@@ -7188,9 +7009,9 @@ bioinformatics file formats, sequence alignment, and more.")
"0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b"))))
(build-system python-build-system)
(inputs
- `(("python-biopython" ,python-biopython)))
+ (list python-biopython))
(native-inputs
- `(("python-nose" ,python-nose)))
+ (list python-nose))
(home-page "https://github.com/fhcrc/seqmagick")
(synopsis "Tools for converting and modifying sequence files")
(description
@@ -7228,7 +7049,7 @@ is one that takes arguments.")
(install-file "seqtk" bin)
#t))))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/lh3/seqtk")
(synopsis "Toolkit for processing biological sequences in FASTA/Q format")
(description
@@ -7265,7 +7086,7 @@ optionally compressed by gzip.")
(install-file "snap-aligner" bin)
(install-file "SNAPCommand" bin)))))))
(native-inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "http://snap.cs.berkeley.edu/")
(synopsis "Short read DNA sequence aligner")
(description
@@ -7313,7 +7134,7 @@ of these reads to align data quickly through a hash-based indexing scheme.")
(find-files "rRNA_databases" ".*fasta"))
#t))))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://bioinfo.lifl.fr/RNA/sortmerna/")
(synopsis "Biological sequence analysis tool for NGS reads")
(description
@@ -7395,10 +7216,9 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
#t))
(delete 'configure))))
(native-inputs
- `(("xxd" ,xxd)))
+ (list xxd))
(inputs
- `(("htslib" ,htslib)
- ("zlib" ,zlib)))
+ (list htslib zlib))
(home-page "https://github.com/alexdobin/STAR")
(synopsis "Universal RNA-seq aligner")
(description
@@ -7505,7 +7325,7 @@ sequences.")
(copy-recursively "../bin" bin))))
;; no "configure" script
(delete 'configure))))
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
(home-page "http://subread.sourceforge.net/")
(synopsis "Tool kit for processing next-gen sequencing data")
(description
@@ -7562,8 +7382,7 @@ against local background noises.")
(install-file "stringtie" bin)
#t))))))
(inputs
- `(("samtools" ,samtools-0.1)
- ("zlib" ,zlib)))
+ (list samtools-0.1 zlib))
(home-page "http://ccb.jhu.edu/software/stringtie/")
(synopsis "Transcript assembly and quantification for RNA-Seq data")
(description
@@ -7617,16 +7436,16 @@ Cuffdiff or Ballgown programs.")
;; available.
(delete 'sanity-check))))
(propagated-inputs
- `(("python-sqlalchemy" ,python-sqlalchemy)
- ("python-decorator" ,python-decorator)
- ("python-biopython" ,python-biopython)
- ("python-pandas" ,python-pandas)
- ("python-psycopg2" ,python-psycopg2)
- ("python-fastalite" ,python-fastalite)
- ("python-pyyaml" ,python-pyyaml)
- ("python-six" ,python-six)
- ("python-jinja2" ,python-jinja2)
- ("python-dendropy" ,python-dendropy)))
+ (list python-sqlalchemy
+ python-decorator
+ python-biopython
+ python-pandas
+ python-psycopg2
+ python-fastalite
+ python-pyyaml
+ python-six
+ python-jinja2
+ python-dendropy))
(home-page "https://github.com/fhcrc/taxtastic")
(synopsis "Tools for taxonomic naming and annotation")
(description
@@ -7656,10 +7475,9 @@ profiles, and associated taxonomic information.")
(string-append "PREFIX=" #$output)
(string-append "MANDIR=" #$output "/share/man/man1"))))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(inputs
- `(("perl" ,perl)
- ("zlib" ,zlib)))
+ (list perl zlib))
(home-page "https://vcftools.github.io/")
(synopsis "Tools for working with VCF files")
(description
@@ -7684,8 +7502,7 @@ data in the form of VCF files.")
"1z4mgwqg1j4n5ika08ai8mg9yjyjhf4821jp83v2bgwzxrykqjgr"))))
(build-system gnu-build-system)
(native-inputs
- `(("perl" ,perl)
- ("python" ,python))) ; for tests
+ (list perl python)) ; for tests
(home-page "http://eddylab.org/infernal/")
(synopsis "Inference of RNA alignments")
(description "Infernal (\"INFERence of RNA ALignment\") is a tool for
@@ -7718,15 +7535,15 @@ sequence.")
(properties `((upstream . "presto")))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-deseq2" ,r-deseq2)
- ("r-dplyr" ,r-dplyr)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-tidyr" ,r-tidyr)))
+ (list r-data-table
+ r-deseq2
+ r-dplyr
+ r-matrix
+ r-rcpp
+ r-rcpparmadillo
+ r-reshape2
+ r-rlang
+ r-tidyr))
(home-page "https://github.com/immunogenomics/presto")
(synopsis "Fast Functions for Differential Expression using Wilcox and AUC")
(description "This package performs a fast Wilcoxon rank sum test and
@@ -7749,25 +7566,25 @@ auROC analysis.")
(properties `((upstream-name . "SnapATAC")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bigmemory" ,r-bigmemory)
- ("r-doparallel" ,r-doparallel)
- ("r-dosnow" ,r-dosnow)
- ("r-edger" ,r-edger)
- ("r-foreach" ,r-foreach)
- ("r-genomicranges" ,r-genomicranges)
- ("r-igraph" ,r-igraph)
- ("r-iranges" ,r-iranges)
- ("r-irlba" ,r-irlba)
- ("r-matrix" ,r-matrix)
- ("r-plyr" ,r-plyr)
- ("r-plot3d" ,r-plot3d)
- ("r-rann" ,r-rann)
- ("r-raster" ,r-raster)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rhdf5" ,r-rhdf5)
- ("r-rtsne" ,r-rtsne)
- ("r-scales" ,r-scales)
- ("r-viridis" ,r-viridis)))
+ (list r-bigmemory
+ r-doparallel
+ r-dosnow
+ r-edger
+ r-foreach
+ r-genomicranges
+ r-igraph
+ r-iranges
+ r-irlba
+ r-matrix
+ r-plyr
+ r-plot3d
+ r-rann
+ r-raster
+ r-rcolorbrewer
+ r-rhdf5
+ r-rtsne
+ r-scales
+ r-viridis))
(home-page "https://github.com/r3fang/SnapATAC")
(synopsis "Single nucleus analysis package for ATAC-Seq")
(description
@@ -7812,12 +7629,10 @@ single cell ATAC-seq sequencing data.")
(("\"perl")
(string-append "\"" (which "perl")))))))))
(inputs
- `(("perl" ,perl)
- ("bowtie" ,bowtie)))
+ (list perl bowtie))
(propagated-inputs
- `(("r-misha" ,r-misha)
- ("r-zoo" ,r-zoo)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-misha r-zoo))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/tanaylab/umi4cpackage")
(synopsis "Processing and analysis of UMI-4C contact profiles")
(description "This is a package that lets you process UMI-4C data from
@@ -7844,16 +7659,16 @@ scratch to produce nice plots.")
(properties `((upstream-name . "ShinyCell")))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-ggplot2" ,r-ggplot2)
- ("r-glue" ,r-glue)
- ("r-gridextra" ,r-gridextra)
- ("r-hdf5r" ,r-hdf5r)
- ("r-matrix" ,r-matrix)
- ("r-r-utils" ,r-r-utils)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-readr" ,r-readr)
- ("r-reticulate" ,r-reticulate)))
+ (list r-data-table
+ r-ggplot2
+ r-glue
+ r-gridextra
+ r-hdf5r
+ r-matrix
+ r-r-utils
+ r-rcolorbrewer
+ r-readr
+ r-reticulate))
(home-page "https://github.com/SGDDNB/ShinyCell")
(synopsis "Shiny interactive web apps for single-cell data")
(description
@@ -7880,30 +7695,30 @@ single-cell data.")
(properties `((upstream-name . "ArchR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-chromvar" ,r-chromvar)
- ("r-complexheatmap" ,r-complexheatmap)
- ("r-data-table" ,r-data-table)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-gridextra" ,r-gridextra)
- ("r-gtable" ,r-gtable)
- ("r-gtools" ,r-gtools)
- ("r-magrittr" ,r-magrittr)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-motifmatchr" ,r-motifmatchr)
- ("r-nabor" ,r-nabor)
- ("r-plyr" ,r-plyr)
- ("r-rcpp" ,r-rcpp)
- ("r-rhdf5" ,r-rhdf5)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-uwot" ,r-uwot)))
+ (list r-biocgenerics
+ r-biostrings
+ r-chromvar
+ r-complexheatmap
+ r-data-table
+ r-genomicranges
+ r-ggplot2
+ r-ggrepel
+ r-gridextra
+ r-gtable
+ r-gtools
+ r-magrittr
+ r-matrix
+ r-matrixstats
+ r-motifmatchr
+ r-nabor
+ r-plyr
+ r-rcpp
+ r-rhdf5
+ r-rsamtools
+ r-s4vectors
+ r-stringr
+ r-summarizedexperiment
+ r-uwot))
(home-page "https://github.com/GreenleafLab/ArchR")
(synopsis "Analyze single-cell regulatory chromatin in R")
(description
@@ -7925,21 +7740,21 @@ single-cell data.")
"10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-mgcv" ,r-mgcv)
- ("r-rook" ,r-rook)
- ("r-rjson" ,r-rjson)
- ("r-cairo" ,r-cairo)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-edger" ,r-edger)
- ("r-quantreg" ,r-quantreg)
- ("r-nnet" ,r-nnet)
- ("r-rmtstat" ,r-rmtstat)
- ("r-extremes" ,r-extremes)
- ("r-pcamethods" ,r-pcamethods)
- ("r-biocparallel" ,r-biocparallel)
- ("r-flexmix" ,r-flexmix)))
+ (list r-rcpp
+ r-rcpparmadillo
+ r-mgcv
+ r-rook
+ r-rjson
+ r-cairo
+ r-rcolorbrewer
+ r-edger
+ r-quantreg
+ r-nnet
+ r-rmtstat
+ r-extremes
+ r-pcamethods
+ r-biocparallel
+ r-flexmix))
(home-page "https://hms-dbmi.github.io/scde/")
(synopsis "R package for analyzing single-cell RNA-seq data")
(description "The SCDE package implements a set of statistical methods for
@@ -7981,7 +7796,7 @@ of transcriptional heterogeneity among single cells.")
(assoc-ref inputs "kentutils")
"/bin/bigWigToWig"))))))))
(inputs
- `(("kentutils" ,kentutils)))
+ (list kentutils))
(home-page "https://github.com/tanaylab/misha")
(synopsis "Toolkit for analysis of genomic data")
(description "This package is intended to help users to efficiently
@@ -8009,18 +7824,18 @@ analyze genomic data resulting from various experiments.")
'(delete-file "inst/doc/shaman-package.R"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-domc" ,r-domc)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gviz" ,r-gviz)
- ("r-misha" ,r-misha)
- ("r-plyr" ,r-plyr)
- ("r-rann" ,r-rann)
- ("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ;; For vignettes
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-knitr" ,r-knitr)))
+ (list r-data-table
+ r-domc
+ r-ggplot2
+ r-gviz
+ r-misha
+ r-plyr
+ r-rann
+ r-rcpp
+ r-reshape2
+ ;; For vignettes
+ r-rmarkdown
+ r-knitr))
(home-page "https://github.com/tanaylab/shaman")
(synopsis "Sampling HiC contact matrices for a-parametric normalization")
(description "The Shaman package implements functions for
@@ -8075,11 +7890,7 @@ information as possible.")
(properties `((upstream-name . "deMULTIplex")))
(build-system r-build-system)
(propagated-inputs
- `(("r-kernsmooth" ,r-kernsmooth)
- ("r-reshape2" ,r-reshape2)
- ("r-rtsne" ,r-rtsne)
- ("r-shortread" ,r-shortread)
- ("r-stringdist" ,r-stringdist)))
+ (list r-kernsmooth r-reshape2 r-rtsne r-shortread r-stringdist))
(home-page "https://github.com/chris-mcginnis-ucsf/MULTI-seq")
(synopsis "MULTI-seq pre-processing and classification tools")
(description
@@ -8118,17 +7929,17 @@ includes software to
(substitute* "requirements.txt"
(("==") ">=")))))))
(inputs
- `(("python-cryptography" ,python-cryptography)
- ("python-intervaltree" ,python-intervaltree)
- ("python-jsonschema" ,python-jsonschema)
- ("python-lxml" ,python-lxml)
- ("python-ndg-httpsclient" ,python-ndg-httpsclient)
- ("python-progressbar2" ,python-progressbar2)
- ("python-pyasn1" ,python-pyasn1)
- ("python-pyopenssl" ,python-pyopenssl)
- ("python-pyyaml" ,python-pyyaml)
- ("python-requests" ,python-requests)
- ("python-termcolor" ,python-termcolor)))
+ (list python-cryptography
+ python-intervaltree
+ python-jsonschema
+ python-lxml
+ python-ndg-httpsclient
+ python-progressbar2
+ python-pyasn1
+ python-pyopenssl
+ python-pyyaml
+ python-requests
+ python-termcolor))
(home-page "https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool")
(synopsis "GDC data transfer tool")
(description "The gdc-client provides several convenience functions over
@@ -8160,12 +7971,9 @@ the GDC API which provides general download/upload via HTTPS.")
#t))))
(build-system gnu-build-system)
(inputs
- `(("zlib" ,zlib)
- ("bzip2" ,bzip2)
- ("cityhash" ,cityhash)))
+ (list zlib bzip2 cityhash))
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)))
+ (list autoconf automake))
(synopsis "Sequence search tools for metagenomics")
(description
"VSEARCH supports DNA sequence searching, clustering, chimera detection,
@@ -8204,8 +8012,7 @@ Needleman-Wunsch).")
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "ParDRe" bin)))))))
(inputs
- `(("openmpi-c++" ,openmpi-c++)
- ("zlib" ,zlib)))
+ (list openmpi-c++ zlib))
(synopsis "Parallel tool to remove duplicate DNA reads")
(description
"ParDRe is a parallel tool to remove duplicate genetic sequence reads.
@@ -8236,7 +8043,7 @@ clusters.")
(build-system cmake-build-system)
(arguments '(#:tests? #false)) ; there are none
(inputs
- `(("boost" ,boost)))
+ (list boost))
(home-page "https://github.com/cbg-ethz/ngshmmalign/")
(synopsis "Profile HMM aligner for NGS reads")
(description
@@ -8282,14 +8089,14 @@ experience substantial biological insertions and deletions.")
(,(getenv "PERL5LIB")))))
scripts)))))))
(inputs
- `(("guile" ,guile-3.0) ; for wrapper scripts
- ("perl" ,perl)
- ("perl-cairo" ,perl-cairo)
- ("perl-data-dumper" ,perl-data-dumper)
- ("perl-digest-md5" ,perl-digest-md5)
- ("perl-getopt-long" ,perl-getopt-long)
- ("perl-json" ,perl-json)
- ("perl-statistics-pca" ,perl-statistics-pca)))
+ (list guile-3.0 ; for wrapper scripts
+ perl
+ perl-cairo
+ perl-data-dumper
+ perl-digest-md5
+ perl-getopt-long
+ perl-json
+ perl-statistics-pca))
(home-page "http://prinseq.sourceforge.net/")
(synopsis "Preprocess sequence data in FASTA or FASTQ formats")
(description
@@ -8340,14 +8147,14 @@ data. It also generates basic statistics for your sequences.")
(when tests?
(invoke "make" "check")))))))
(inputs
- `(("boost" ,boost)
- ("htslib" ,htslib)
- ("python" ,python)
- ("python-biopython" ,python-biopython)
- ("python-numpy" ,python-numpy)
- ("zlib" ,zlib)))
+ (list boost
+ htslib
+ python
+ python-biopython
+ python-numpy
+ zlib))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "")
(synopsis "Short reads assembly into haplotypes")
(description
@@ -8372,11 +8179,9 @@ frequency of the different genetic variants present in a mixed sample.")
(arguments
`(#:test-target "spec"))
(native-inputs
- `(("bundler" ,bundler)
- ("ruby-rspec" ,ruby-rspec)
- ("ruby-rake-compiler" ,ruby-rake-compiler)))
+ (list bundler ruby-rspec ruby-rake-compiler))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
(description
"@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
@@ -8398,7 +8203,7 @@ quality scores.")
"02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
(build-system ruby-build-system)
(native-inputs
- `(("ruby-rspec" ,ruby-rspec)))
+ (list ruby-rspec))
(synopsis "Tool for fast querying of genome locations")
(description
"Bio-locus is a tabix-like tool for fast querying of genome
@@ -8421,10 +8226,9 @@ chr+pos+alt information in a database.")
"1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
(build-system ruby-build-system)
(propagated-inputs
- `(("ruby-bio-logger" ,ruby-bio-logger)
- ("ruby-nokogiri" ,ruby-nokogiri)))
+ (list ruby-bio-logger ruby-nokogiri))
(inputs
- `(("ruby-rspec" ,ruby-rspec)))
+ (list ruby-rspec))
(synopsis "Fast big data BLAST XML parser and library")
(description
"Very fast parallel big-data BLAST XML file parser which can be used as
@@ -8446,9 +8250,9 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
"1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938"))))
(build-system ruby-build-system)
(propagated-inputs
- `(("ruby-libxml" ,ruby-libxml)))
+ (list ruby-libxml))
(native-inputs
- `(("which" ,which))) ; required for test phase
+ (list which)) ; required for test phase
(arguments
`(#:phases
(modify-phases %standard-phases
@@ -8489,7 +8293,7 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
"1glw5pn9s8z13spxk6yyfqaz80n9lga67f33w35nkpq9dwi2vg6g"))))
(build-system ruby-build-system)
(native-inputs
- `(("ruby-cucumber" ,ruby-cucumber)))
+ (list ruby-cucumber))
(synopsis "Smart VCF parser DSL")
(description
"Bio-vcf provides a @acronym{DSL, domain specific language} for processing
@@ -8532,16 +8336,16 @@ including VCF header and contents in RDF and JSON.")
(inputs
`(("r" ,r-minimal)))
(propagated-inputs
- `(("r-catools" ,r-catools)
- ("r-snow" ,r-snow)
- ("r-snowfall" ,r-snowfall)
- ("r-bitops" ,r-bitops)
- ("r-rsamtools" ,r-rsamtools)
- ("r-spp" ,r-spp)
- ("gawk" ,gawk)
- ("samtools" ,samtools)
- ("boost" ,boost)
- ("gzip" ,gzip)))
+ (list r-catools
+ r-snow
+ r-snowfall
+ r-bitops
+ r-rsamtools
+ r-spp
+ gawk
+ samtools
+ boost
+ gzip))
(home-page "https://github.com/kundajelab/phantompeakqualtools")
(synopsis "Informative enrichment for ChIP-seq data")
(description "This package computes informative enrichment and quality
@@ -8564,8 +8368,7 @@ characteristic tag shift values in these assays.")
"1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-optparse" ,r-optparse)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-optparse r-rcolorbrewer))
(home-page "https://www.e-rna.org/r-chie/index.cgi")
(synopsis "Analysis framework for RNA secondary structure")
(description
@@ -8617,7 +8420,7 @@ secondary structure and comparative analysis in R.")
("guile-json" ,guile-json-1)
("guile-redis" ,guile2.2-redis)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "https://github.com/BIMSBbioinfo/rcas-web")
(synopsis "Web interface for RNA-centric annotation system (RCAS)")
(description "This package provides a simple web interface for the
@@ -8642,16 +8445,16 @@ secondary structure and comparative analysis in R.")
"14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-iranges" ,r-iranges)
- ("r-xvector" ,r-xvector)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-gtools" ,r-gtools)
- ("r-genomicranges" ,r-genomicranges)
- ("r-sfsmisc" ,r-sfsmisc)
- ("r-kernlab" ,r-kernlab)
- ("r-s4vectors" ,r-s4vectors)
- ("r-biocgenerics" ,r-biocgenerics)))
+ (list r-iranges
+ r-xvector
+ r-biostrings
+ r-bsgenome
+ r-gtools
+ r-genomicranges
+ r-sfsmisc
+ r-kernlab
+ r-s4vectors
+ r-biocgenerics))
(home-page "https://github.com/ManuSetty/ChIPKernels")
(synopsis "Build string kernels for DNA Sequence analysis")
(description "ChIPKernels is an R package for building different string
@@ -8676,12 +8479,12 @@ Sequences.")
"1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-chipkernels" ,r-chipkernels)
- ("r-genomicranges" ,r-genomicranges)
- ("r-spams" ,r-spams)
- ("r-wgcna" ,r-wgcna)
- ("r-fastcluster" ,r-fastcluster)))
+ (list r-biostrings
+ r-chipkernels
+ r-genomicranges
+ r-spams
+ r-wgcna
+ r-fastcluster))
(home-page "https://github.com/ManuSetty/SeqGL")
(synopsis "Group lasso for Dnase/ChIP-seq data")
(description "SeqGL is a group lasso based algorithm to extract
@@ -8731,17 +8534,14 @@ AM_CONDITIONAL(AMPNG, true)"))
(add-after 'disable-update-check 'autogen
(lambda _ (invoke "autoreconf" "-vif") #t)))))
(inputs
- `(("perl" ,perl)
- ("libpng" ,libpng)
- ("gd" ,gd)
- ("libx11" ,libx11)
- ("libharu" ,libharu)
- ("zlib" ,zlib)))
+ (list perl
+ libpng
+ gd
+ libx11
+ libharu
+ zlib))
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("libtool" ,libtool)
- ("pkg-config" ,pkg-config)))
+ (list autoconf automake libtool pkg-config))
(home-page "http://emboss.sourceforge.net")
(synopsis "Molecular biology analysis suite")
(description "EMBOSS is the \"European Molecular Biology Open Software
@@ -8789,8 +8589,7 @@ tools for sequence analysis into a seamless whole.")
"bin" (string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(inputs
- `(("gsl" ,gsl)
- ("zlib" ,zlib)))
+ (list gsl zlib))
(home-page "https://github.com/arq5x/bits")
(synopsis "Implementation of binary interval search algorithm")
(description "This package provides an implementation of the
@@ -8880,9 +8679,7 @@ may optionally be provided to further inform the peak-calling process.")
`(#:python ,python-2 ; python2 only
#:tests? #f)) ; no tests included
(propagated-inputs
- `(("python2-numpy" ,python2-numpy)
- ("python2-scipy" ,python2-scipy)
- ("python2-pysam" ,python2-pysam)))
+ (list python2-numpy python2-scipy python2-pysam))
(home-page "https://github.com/shawnzhangyx/PePr")
(synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
(description
@@ -8957,20 +8754,20 @@ replacement for strverscmp.")
;; reasons.
(delete 'sanity-check))))
(propagated-inputs
- `(("python-click" ,python-click)
- ("python-coloredlogs" ,python-coloredlogs)
- ("python-future" ,python-future)
- ("python-jinja2" ,python-jinja2)
- ("python-lzstring" ,python-lzstring)
- ("python-markdown" ,python-markdown)
- ("python-matplotlib" ,python-matplotlib)
- ("python-networkx" ,python-networkx)
- ("python-numpy" ,python-numpy)
- ("python-pyyaml" ,python-pyyaml)
- ("python-requests" ,python-requests)
- ("python-rich" ,python-rich)
- ("python-simplejson" ,python-simplejson)
- ("python-spectra" ,python-spectra)))
+ (list python-click
+ python-coloredlogs
+ python-future
+ python-jinja2
+ python-lzstring
+ python-markdown
+ python-matplotlib
+ python-networkx
+ python-numpy
+ python-pyyaml
+ python-requests
+ python-rich
+ python-simplejson
+ python-spectra))
(native-inputs
`(("python-pytest" ,python-pytest)
("tests"
@@ -9009,19 +8806,16 @@ common bioinformatics tools.")
"12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
(build-system python-build-system)
(inputs
- `(("boost" ,boost)
- ("c-blosc" ,c-blosc)
- ("gsl" ,gsl)
- ("hdf5" ,hdf5)
- ("hdf5-blosc" ,hdf5-blosc)
- ("python-cython" ,python-cython)
- ("zlib" ,zlib)))
+ (list boost
+ c-blosc
+ gsl
+ hdf5
+ hdf5-blosc
+ python-cython
+ zlib))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-pycurl" ,python-pycurl)
- ("python-pyzmq" ,python-pyzmq)
- ("python-scipy" ,python-scipy)
- ("python-tables" ,python-tables)))
+ (list python-numpy python-pycurl python-pyzmq python-scipy
+ python-tables))
(home-page "https://vatlab.github.io/vat-docs/")
(synopsis "Analyze genetic variants from Next-Gen sequencing studies")
(description
@@ -9047,11 +8841,7 @@ manipulate and analyze genetic variants.")
(properties `((upstream-name . "RareMETALS2")))
(build-system r-build-system)
(propagated-inputs
- `(("r-seqminer" ,r-seqminer)
- ("r-mvtnorm" ,r-mvtnorm)
- ("r-mass" ,r-mass)
- ("r-compquadform" ,r-compquadform)
- ("r-getopt" ,r-getopt)))
+ (list r-seqminer r-mvtnorm r-mass r-compquadform r-getopt))
(home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
(synopsis "Analyze gene-level association tests for binary trait")
(description
@@ -9082,11 +8872,7 @@ trait.")
"0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-ggplot2" ,r-ggplot2)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-gridextra" ,r-gridextra)
- ("r-gplots" ,r-gplots)
- ("r-plyr" ,r-plyr)))
+ (list r-ggplot2 r-rcolorbrewer r-gridextra r-gplots r-plyr))
(home-page "https://github.com/rajewsky-lab/dropbead")
(synopsis "Basic exploration and analysis of Drop-seq data")
(description "This package offers a quick and straight-forward way to
@@ -9118,41 +8904,41 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(properties `((upstream-name . "CellChat")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-circlize" ,r-circlize)
- ("r-colorspace" ,r-colorspace)
- ("r-complexheatmap" ,r-complexheatmap)
- ("r-cowplot" ,r-cowplot)
- ("r-dplyr" ,r-dplyr)
- ("r-expm" ,r-expm)
- ("r-fnn" ,r-fnn)
- ("r-forcats" ,r-forcats)
- ("r-future" ,r-future)
- ("r-future-apply" ,r-future-apply)
- ("r-gg-gap" ,r-gg-gap)
- ("r-ggalluvial" ,r-ggalluvial)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-magrittr" ,r-magrittr)
- ("r-matrix" ,r-matrix)
- ("r-nmf" ,r-nmf)
- ("r-patchwork" ,r-patchwork)
- ("r-pbapply" ,r-pbapply)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-reshape2" ,r-reshape2)
- ("r-reticulate" ,r-reticulate)
- ("r-rspectra" ,r-rspectra)
- ("r-rtsne" ,r-rtsne)
- ("r-scales" ,r-scales)
- ("r-shape" ,r-shape)
- ("r-sna" ,r-sna)
- ("r-stringr" ,r-stringr)
- ("r-svglite" ,r-svglite)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-circlize
+ r-colorspace
+ r-complexheatmap
+ r-cowplot
+ r-dplyr
+ r-expm
+ r-fnn
+ r-forcats
+ r-future
+ r-future-apply
+ r-gg-gap
+ r-ggalluvial
+ r-ggplot2
+ r-ggrepel
+ r-igraph
+ r-irlba
+ r-magrittr
+ r-matrix
+ r-nmf
+ r-patchwork
+ r-pbapply
+ r-rcolorbrewer
+ r-rcpp
+ r-rcppeigen
+ r-reshape2
+ r-reticulate
+ r-rspectra
+ r-rtsne
+ r-scales
+ r-shape
+ r-sna
+ r-stringr
+ r-svglite))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/sqjin/CellChat")
(synopsis "Analysis of cell-cell communication from single-cell transcriptomics data")
(description
@@ -9198,11 +8984,9 @@ communication networks from scRNA-seq data.")
(copy-file (string-append "bin/sambamba-" ,version)
(string-append bin "/sambamba"))))))))
(native-inputs
- `(("python" ,python)))
+ (list python))
(inputs
- `(("ldc" ,ldc)
- ("lz4" ,lz4)
- ("zlib" ,zlib)))
+ (list ldc lz4 zlib))
(home-page "https://github.com/biod/sambamba")
(synopsis "Tools for working with SAM/BAM data")
(description "Sambamba is a high performance modern robust and
@@ -9245,10 +9029,7 @@ sort, markdup, and depth.")
(install-file "bin/Ritornello" bin)
#t))))))
(inputs
- `(("samtools" ,samtools-0.1)
- ("fftw" ,fftw)
- ("boost" ,boost)
- ("zlib" ,zlib)))
+ (list samtools-0.1 fftw boost zlib))
(home-page "https://github.com/KlugerLab/Ritornello")
(synopsis "Control-free peak caller for ChIP-seq data")
(description "Ritornello is a ChIP-seq peak calling algorithm based on
@@ -9314,12 +9095,9 @@ with narrow binding events such as transcription factor ChIP-seq.")
(install-file "trim_galore" bin)
#t))))))
(inputs
- `(("gzip" ,gzip)
- ("perl" ,perl)
- ("pigz" ,pigz)
- ("cutadapt" ,cutadapt)))
+ (list gzip perl pigz cutadapt))
(native-inputs
- `(("unzip" ,unzip)))
+ (list unzip))
(home-page "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
(synopsis "Wrapper around Cutadapt and FastQC")
(description "Trim Galore! is a wrapper script to automate quality and
@@ -9465,22 +9243,19 @@ programs for inferring phylogenies (evolutionary trees).")
`(("python" ,python-wrapper)
("swig" ,swig)))
(inputs
- `(("boost" ,boost)
- ("cgal" ,cgal)
- ("gsl" ,gsl)
- ("hdf5" ,hdf5)
- ("fftw" ,fftw)
- ("eigen" ,eigen)
- ;; Enabling MPI causes the build to use all the available memory and
- ;; fail (tested on a machine with 32 GiB of RAM).
- ;;("mpi" ,openmpi)
- ("opencv" ,opencv)))
+ (list boost
+ cgal
+ gsl
+ hdf5
+ fftw
+ eigen
+ ;; Enabling MPI causes the build to use all the available memory and
+ ;; fail (tested on a machine with 32 GiB of RAM).
+ ;;("mpi" ,openmpi)
+ opencv))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)
- ("python-pandas" ,python-pandas)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-networkx" ,python-networkx)))
+ (list python-numpy python-scipy python-pandas python-scikit-learn
+ python-networkx))
(home-page "https://integrativemodeling.org")
(synopsis "Integrative modeling platform")
(description "IMP's broad goal is to contribute to a comprehensive
@@ -9538,18 +9313,18 @@ applications for tackling some common problems in a user-friendly way.")
(add-installed-pythonpath inputs outputs)
(invoke "python3" "test/test_all.py")))))))
(native-inputs
- `(("glib" ,glib "bin") ;for gtester
- ("pkg-config" ,pkg-config)))
+ (list `(,glib "bin") ;for gtester
+ pkg-config))
(inputs
;; TODO: add Chimera for visualization
- `(("imp" ,imp)
- ("mcl" ,mcl)
- ("python-future" ,python-future)
- ("python-h5py" ,python-h5py)
- ("python-scipy" ,python-scipy)
- ("python-numpy" ,python-numpy)
- ("python-matplotlib" ,python-matplotlib)
- ("python-pysam" ,python-pysam)))
+ (list imp
+ mcl
+ python-future
+ python-h5py
+ python-scipy
+ python-numpy
+ python-matplotlib
+ python-pysam))
(home-page "https://3dgenomes.github.io/TADbit/")
(synopsis "Analyze, model, and explore 3C-based data")
(description
@@ -9728,8 +9503,7 @@ browser.")
(install-file "build~/fseq.jar" lib)
(copy-recursively "lib" lib)))))))
(inputs
- `(("perl" ,perl)
- ("java-commons-cli" ,java-commons-cli)))
+ (list perl java-commons-cli))
(home-page "https://fureylab.web.unc.edu/software/fseq/")
(synopsis "Feature density estimator for high-throughput sequence tags")
(description
@@ -9815,9 +9589,7 @@ Browser.")
"/bin/gunzip -c")))
#t))))))
(inputs
- `(("gzip" ,gzip)
- ("perl-carp" ,perl-carp)
- ("perl-getopt-long" ,perl-getopt-long)))
+ (list gzip perl-carp perl-getopt-long))
(native-inputs
`(("plotly.js"
,(origin
@@ -9926,11 +9698,9 @@ using nucleotide or amino-acid sequence data.")
(install-file exe bin))
exes)))))))
(inputs
- `(("htslib" ,htslib)
- ("ncurses" ,ncurses)
- ("zlib" ,zlib)))
+ (list htslib ncurses zlib))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "https://www.bioinf.uni-leipzig.de/Software/segemehl")
(synopsis "Map short sequencer reads to reference genomes")
(description "Segemehl is software to map short sequencer reads to
@@ -9979,9 +9749,7 @@ output of segemehl is a SAM or BAM formatted alignment file.")
(("include_directories\\(\\.\\./ext/htslib\\)") ""))
#t)))))
(inputs
- `(("hdf5" ,hdf5)
- ("htslib" ,htslib-1.9)
- ("zlib" ,zlib)))
+ (list hdf5 htslib-1.9 zlib))
(home-page "https://pachterlab.github.io/kallisto/")
(synopsis "Near-optimal RNA-Seq quantification")
(description
@@ -10147,7 +9915,7 @@ dependency like SeqAn.")
("tbb" ,tbb-2020)
("zlib" ,zlib)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "https://www.cs.cmu.edu/~ckingsf/software/sailfish/")
(synopsis "Mapping-based isoform quantification from RNA-Seq reads")
(description "Sailfish is a tool for genomic transcript quantification
@@ -10322,7 +10090,7 @@ The following file formats are supported:
("xz" ,xz)
("zlib" ,zlib)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "https://github.com/COMBINE-lab/salmon")
(synopsis "Quantification from RNA-seq reads using lightweight alignments")
(description "Salmon is a program to produce highly-accurate,
@@ -10355,12 +10123,9 @@ variational inference.")
(lambda _
(invoke "pytest" "tests"))))))
(propagated-inputs
- `(("python-h5py" ,python-h5py)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-scipy" ,python-scipy)))
+ (list python-h5py python-numpy python-pandas python-scipy))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-pytest))
(home-page "https://github.com/linnarsson-lab/loompy")
(synopsis "Work with .loom files for single-cell RNA-seq data")
(description "The loom file format is an efficient format for very large
@@ -10382,7 +10147,7 @@ single-cell RNA-seq data.")
(base32 "0bccs37d5saxn5xsd2rfpkrnc5a120xs3ibizai66fgvp1vxbnc4"))))
(build-system python-build-system)
(arguments `(#:tests? #false)) ; require internet access
- (propagated-inputs `(("python-requests" ,python-requests)))
+ (propagated-inputs (list python-requests))
(home-page "https://github.com/biothings/biothings_client.py")
(synopsis "Python client for BioThings API services")
(description "This package provides a Python client for BioThings
@@ -10401,7 +10166,7 @@ API services.")
(base32 "1snszwdgfygchxshcbry3b5pbcw3g1isp8dw46razxccqaxwlag7"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-biothings-client" ,python-biothings-client)))
+ (list python-biothings-client))
(home-page "https://github.com/biothings/mygene.py")
(synopsis "Python Client for MyGene.Info services.")
(description "MyGene.Info provides simple-to-use REST web services
@@ -10477,8 +10242,7 @@ MyGene.Info services.")
;; There is no install target
(replace 'install (install-jars ".")))))
(propagated-inputs
- `(("java-commons-codec" ,java-commons-codec)
- ("java-openchart2" ,java-openchart2)))
+ (list java-commons-codec java-openchart2))
(home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
(synopsis "Phylogenomics libraries for Java")
(description "Forester is a collection of Java libraries for
@@ -10550,8 +10314,7 @@ reading, writing, and exporting phylogenetic trees.")
;; There is no install target
(replace 'install (install-jars ".")))))
(propagated-inputs
- `(("java-commons-codec" ,java-commons-codec)
- ("java-openchart2" ,java-openchart2)))
+ (list java-commons-codec java-openchart2))
;; The source archive does not contain the resources.
(native-inputs
`(("phyloxml.xsd"
@@ -10619,13 +10382,10 @@ reading, writing, and exporting phylogenetic trees.")
"build/test-classes")
#t)))))
(propagated-inputs
- `(("java-log4j-api" ,java-log4j-api)
- ("java-log4j-core" ,java-log4j-core)
- ("java-slf4j-api" ,java-slf4j-api)
- ("java-slf4j-simple" ,java-slf4j-simple)))
+ (list java-log4j-api java-log4j-core java-slf4j-api
+ java-slf4j-simple))
(native-inputs
- `(("java-junit" ,java-junit)
- ("java-hamcrest-core" ,java-hamcrest-core)))
+ (list java-junit java-hamcrest-core))
(home-page "https://biojava.org")
(synopsis "Core libraries of Java framework for processing biological data")
(description "BioJava is a project dedicated to providing a Java framework
@@ -10660,15 +10420,14 @@ This package provides the core libraries.")
"build/test-classes")
#t)))))
(propagated-inputs
- `(("java-log4j-api" ,java-log4j-api)
- ("java-log4j-core" ,java-log4j-core)
- ("java-slf4j-api" ,java-slf4j-api)
- ("java-slf4j-simple" ,java-slf4j-simple)
- ("java-biojava-core" ,java-biojava-core)
- ("java-forester" ,java-forester)))
- (native-inputs
- `(("java-junit" ,java-junit)
- ("java-hamcrest-core" ,java-hamcrest-core)))
+ (list java-log4j-api
+ java-log4j-core
+ java-slf4j-api
+ java-slf4j-simple
+ java-biojava-core
+ java-forester))
+ (native-inputs
+ (list java-junit java-hamcrest-core))
(home-page "https://biojava.org")
(synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the
@@ -10696,16 +10455,15 @@ forester phylogenomics library for constructing phylogenetic trees.")))
"build/test-classes")
#t)))))
(propagated-inputs
- `(("java-log4j-api" ,java-log4j-api)
- ("java-log4j-core" ,java-log4j-core)
- ("java-slf4j-api" ,java-slf4j-api)
- ("java-slf4j-simple" ,java-slf4j-simple)
- ("java-biojava-core" ,java-biojava-core)
- ("java-biojava-phylo" ,java-biojava-phylo)
- ("java-forester" ,java-forester)))
- (native-inputs
- `(("java-junit" ,java-junit)
- ("java-hamcrest-core" ,java-hamcrest-core)))
+ (list java-log4j-api
+ java-log4j-core
+ java-slf4j-api
+ java-slf4j-simple
+ java-biojava-core
+ java-biojava-phylo
+ java-forester))
+ (native-inputs
+ (list java-junit java-hamcrest-core))
(home-page "https://biojava.org")
(synopsis "Biojava API for genetic sequence alignment")
(description "The alignment module of BioJava provides an API that
@@ -10754,15 +10512,14 @@ contains
"build/test-classes")
#t)))))
(propagated-inputs
- `(("java-log4j-api" ,java-log4j-api)
- ("java-log4j-core" ,java-log4j-core)
- ("java-slf4j-api" ,java-slf4j-api)
- ("java-slf4j-simple" ,java-slf4j-simple)
- ("java-biojava-core" ,java-biojava-core-4.0)
- ("java-forester" ,java-forester-1.005)))
- (native-inputs
- `(("java-junit" ,java-junit)
- ("java-hamcrest-core" ,java-hamcrest-core)))
+ (list java-log4j-api
+ java-log4j-core
+ java-slf4j-api
+ java-slf4j-simple
+ java-biojava-core-4.0
+ java-forester-1.005))
+ (native-inputs
+ (list java-junit java-hamcrest-core))
(home-page "https://biojava.org")
(synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the
@@ -10790,16 +10547,15 @@ forester phylogenomics library for constructing phylogenetic trees.")))
"build/test-classes")
#t)))))
(propagated-inputs
- `(("java-log4j-api" ,java-log4j-api)
- ("java-log4j-core" ,java-log4j-core)
- ("java-slf4j-api" ,java-slf4j-api)
- ("java-slf4j-simple" ,java-slf4j-simple)
- ("java-biojava-core" ,java-biojava-core-4.0)
- ("java-biojava-phylo" ,java-biojava-phylo-4.0)
- ("java-forester" ,java-forester-1.005)))
- (native-inputs
- `(("java-junit" ,java-junit)
- ("java-hamcrest-core" ,java-hamcrest-core)))
+ (list java-log4j-api
+ java-log4j-core
+ java-slf4j-api
+ java-slf4j-simple
+ java-biojava-core-4.0
+ java-biojava-phylo-4.0
+ java-forester-1.005))
+ (native-inputs
+ (list java-junit java-hamcrest-core))
(home-page "https://biojava.org")
(synopsis "Biojava API for genetic sequence alignment")
(description "The alignment module of BioJava provides an API that
@@ -10940,8 +10696,7 @@ contains
("java-simple-xml" ,java-simple-xml)
("java-snakeyaml" ,java-snakeyaml)))
(native-inputs
- `(("unzip" ,unzip)
- ("java-testng" ,java-testng)))
+ (list unzip java-testng))
(home-page "http://mccarrolllab.com/dropseq/")
(synopsis "Tools for Drop-seq analyses")
(description "Drop-seq is a technology to enable biologists to
@@ -10985,44 +10740,42 @@ once. This package provides tools to perform Drop-seq analyses.")
(search-input-directory inputs
"share/zoneinfo")))))))
(inputs
- `(("coreutils" ,coreutils)
- ("sed" ,sed)
- ("gzip" ,gzip)
- ("snakemake" ,snakemake)
- ("multiqc" ,multiqc)
- ("star" ,star-for-pigx)
- ("hisat2" ,hisat2)
- ("fastp" ,fastp)
- ("htseq" ,htseq)
- ("samtools" ,samtools)
- ("r-minimal" ,r-minimal)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggpubr" ,r-ggpubr)
- ("r-ggrepel" ,r-ggrepel)
- ("r-gprofiler2" ,r-gprofiler2)
- ("r-deseq2" ,r-deseq2)
- ("r-dt" ,r-dt)
- ("r-knitr" ,r-knitr)
- ("r-pheatmap" ,r-pheatmap)
- ("r-corrplot" ,r-corrplot)
- ("r-reshape2" ,r-reshape2)
- ("r-plotly" ,r-plotly)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-crosstalk" ,r-crosstalk)
- ("r-tximport" ,r-tximport)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-rjson" ,r-rjson)
- ("salmon" ,salmon)
- ("pandoc" ,pandoc)
- ("python-wrapper" ,python-wrapper)
- ("python-deeptools" ,python-deeptools)
- ("python-pyyaml" ,python-pyyaml)))
- (native-inputs
- `(("tzdata" ,tzdata)
- ("automake" ,automake)
- ("autoconf" ,autoconf)))
+ (list coreutils
+ sed
+ gzip
+ snakemake
+ multiqc
+ star-for-pigx
+ hisat2
+ fastp
+ htseq
+ samtools
+ r-minimal
+ r-rmarkdown
+ r-ggplot2
+ r-ggpubr
+ r-ggrepel
+ r-gprofiler2
+ r-deseq2
+ r-dt
+ r-knitr
+ r-pheatmap
+ r-corrplot
+ r-reshape2
+ r-plotly
+ r-scales
+ r-summarizedexperiment
+ r-crosstalk
+ r-tximport
+ r-rtracklayer
+ r-rjson
+ salmon
+ pandoc
+ python-wrapper
+ python-deeptools
+ python-pyyaml))
+ (native-inputs
+ (list tzdata automake autoconf))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for RNA sequencing experiments")
(description "PiGX RNAseq is an analysis pipeline for preprocessing and
@@ -11055,58 +10808,56 @@ expression report comparing samples in an easily configurable manner.")
(lambda _
(invoke "autoreconf" "-vif"))))))
(inputs
- `(("grep" ,grep)
- ("coreutils" ,coreutils)
- ("r-minimal" ,r-minimal)
- ("r-argparser" ,r-argparser)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-chipseq" ,r-chipseq)
- ("r-corrplot" ,r-corrplot)
- ("r-data-table" ,r-data-table)
- ("r-deseq2" ,r-deseq2)
- ("r-dplyr" ,r-dplyr)
- ("r-dt" ,r-dt)
- ("r-genomation" ,r-genomation)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-gprofiler2" ,r-gprofiler2)
- ("r-heatmaply" ,r-heatmaply)
- ("r-hexbin" ,r-hexbin)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-jsonlite" ,r-jsonlite)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plotly" ,r-plotly)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rsubread" ,r-rsubread)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("python-wrapper" ,python-wrapper)
- ("python-pyyaml" ,python-pyyaml)
- ("python-magic" ,python-magic)
- ("python-xlrd" ,python-xlrd)
- ("trim-galore" ,trim-galore)
- ("macs" ,macs)
- ("multiqc" ,multiqc)
- ("perl" ,perl)
- ("pandoc" ,pandoc)
- ("fastqc" ,fastqc)
- ("bowtie" ,bowtie)
- ("idr" ,idr)
- ("snakemake" ,snakemake)
- ("samtools" ,samtools)
- ("bedtools" ,bedtools)
- ("kentutils" ,kentutils)))
- (native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("python-pytest" ,python-pytest)))
+ (list grep
+ coreutils
+ r-minimal
+ r-argparser
+ r-biocparallel
+ r-biostrings
+ r-chipseq
+ r-corrplot
+ r-data-table
+ r-deseq2
+ r-dplyr
+ r-dt
+ r-genomation
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-ggrepel
+ r-gprofiler2
+ r-heatmaply
+ r-hexbin
+ r-htmlwidgets
+ r-jsonlite
+ r-pheatmap
+ r-plotly
+ r-rmarkdown
+ r-rsamtools
+ r-rsubread
+ r-rtracklayer
+ r-s4vectors
+ r-stringr
+ r-tibble
+ r-tidyr
+ python-wrapper
+ python-pyyaml
+ python-magic
+ python-xlrd
+ trim-galore
+ macs
+ multiqc
+ perl
+ pandoc
+ fastqc
+ bowtie
+ idr
+ snakemake
+ samtools
+ bedtools
+ kentutils))
+ (native-inputs
+ (list autoconf automake python-pytest))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for ChIP sequencing experiments")
(description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
@@ -11149,41 +10900,39 @@ in an easily configurable manner.")
(search-input-directory inputs
"share/zoneinfo")))))))
(native-inputs
- `(("tzdata" ,tzdata)
- ("automake" ,automake)
- ("autoconf" ,autoconf)))
- (inputs
- `(("coreutils" ,coreutils)
- ("sed" ,sed)
- ("grep" ,grep)
- ("r-minimal" ,r-minimal)
- ("r-annotationhub" ,r-annotationhub)
- ("r-dt" ,r-dt)
- ("r-genomation" ,r-genomation)
- ("r-ggbio" ,r-ggbio)
- ("r-ggrepel" ,r-ggrepel)
- ("r-matrixstats" ,r-matrixstats)
- ("r-methylkit" ,r-methylkit)
- ("r-reshape2" ,r-reshape2)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-bookdown" ,r-bookdown)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggbio" ,r-ggbio)
- ("pandoc" ,pandoc)
- ("python-wrapper" ,python-wrapper)
- ("python-pyyaml" ,python-pyyaml)
- ("snakemake" ,snakemake)
- ("bismark" ,bismark)
- ("bowtie" ,bowtie)
- ("bwa-meth" ,bwa-meth)
- ("fastqc" ,fastqc)
- ("methyldackel" ,methyldackel)
- ("multiqc" ,multiqc)
- ("trim-galore" ,trim-galore)
- ("cutadapt" ,cutadapt)
- ("samblaster" ,samblaster)
- ("samtools" ,samtools)))
+ (list tzdata automake autoconf))
+ (inputs
+ (list coreutils
+ sed
+ grep
+ r-minimal
+ r-annotationhub
+ r-dt
+ r-genomation
+ r-ggbio
+ r-ggrepel
+ r-matrixstats
+ r-methylkit
+ r-reshape2
+ r-rtracklayer
+ r-rmarkdown
+ r-bookdown
+ r-ggplot2
+ r-ggbio
+ pandoc
+ python-wrapper
+ python-pyyaml
+ snakemake
+ bismark
+ bowtie
+ bwa-meth
+ fastqc
+ methyldackel
+ multiqc
+ trim-galore
+ cutadapt
+ samblaster
+ samtools))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
(description "PiGx BSseq is a data processing pipeline for raw fastq read
@@ -11213,8 +10962,7 @@ methylation and segmentation.")
(lambda _
(invoke "autoreconf" "-vif"))))))
(native-inputs
- `(("automake" ,automake)
- ("autoconf" ,autoconf)))
+ (list automake autoconf))
(inputs
`(("coreutils" ,coreutils)
("perl" ,perl)
@@ -11288,40 +11036,39 @@ based methods.")
(lambda _
(invoke "autoreconf" "-vif"))))))
(native-inputs
- `(("automake" ,automake)
- ("autoconf" ,autoconf)))
- (inputs
- `(("bash-minimal" ,bash-minimal)
- ("bbmap" ,bbmap)
- ("bedtools" ,bedtools)
- ("bwa" ,bwa)
- ("ensembl-vep" ,ensembl-vep)
- ("fastp" ,fastp)
- ("fastqc" ,fastqc)
- ("ivar" ,ivar)
- ("kraken2" ,kraken2)
- ("krona-tools" ,krona-tools)
- ("lofreq" ,lofreq)
- ("multiqc" ,multiqc)
- ("prinseq" ,prinseq)
- ("python-pyyaml" ,python-pyyaml)
- ("python-wrapper" ,python-wrapper)
- ("r-base64url" ,r-base64url)
- ("r-dplyr" ,r-dplyr)
- ("r-dt" ,r-dt)
- ("r-ggplot2" ,r-ggplot2)
- ("r-magrittr" ,r-magrittr)
- ("r-minimal" ,r-minimal)
- ("r-plotly" ,r-plotly)
- ("r-qpcr" ,r-qpcr)
- ("r-r-utils" ,r-r-utils)
- ("r-reshape2" ,r-reshape2)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-stringr" ,r-stringr)
- ("r-tidyr" ,r-tidyr)
- ("samtools" ,samtools)
- ("snakemake" ,snakemake)
- ("wget" ,wget)))
+ (list automake autoconf))
+ (inputs
+ (list bash-minimal
+ bbmap
+ bedtools
+ bwa
+ ensembl-vep
+ fastp
+ fastqc
+ ivar
+ kraken2
+ krona-tools
+ lofreq
+ multiqc
+ prinseq
+ python-pyyaml
+ python-wrapper
+ r-base64url
+ r-dplyr
+ r-dt
+ r-ggplot2
+ r-magrittr
+ r-minimal
+ r-plotly
+ r-qpcr
+ r-r-utils
+ r-reshape2
+ r-rmarkdown
+ r-stringr
+ r-tidyr
+ samtools
+ snakemake
+ wget))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for wastewater sequencing")
(description "PiGx SARS-CoV-2 is a pipeline for analysing data from
@@ -11345,11 +11092,7 @@ variant abundance over time and location.")
"1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7"))))
(build-system gnu-build-system)
(inputs
- `(("python" ,python)
- ("pigx-bsseq" ,pigx-bsseq)
- ("pigx-chipseq" ,pigx-chipseq)
- ("pigx-rnaseq" ,pigx-rnaseq)
- ("pigx-scrnaseq" ,pigx-scrnaseq)))
+ (list python pigx-bsseq pigx-chipseq pigx-rnaseq pigx-scrnaseq))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipelines for genomics")
(description "PiGx is a collection of genomics pipelines. It includes the
@@ -11391,7 +11134,7 @@ HTML reports with interesting findings about your samples.")
(install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/jsh58/Genrich")
(synopsis "Detecting sites of genomic enrichment")
(description "Genrich is a peak-caller for genomic enrichment
@@ -11421,11 +11164,9 @@ enrichment.")
'(#:tests? #f ; there are none
#:configure-flags (list "-DNH=ON"))) ; do not use SSE4.2 instructions
(inputs
- `(("sdsl-lite" ,sdsl-lite)
- ("openssl" ,openssl)
- ("zlib" ,zlib)))
+ (list sdsl-lite openssl zlib))
(native-inputs
- `(("gcc" ,gcc-7)))
+ (list gcc-7))
(home-page "https://github.com/splatlab/mantis")
(synopsis "Large-scale sequence-search index data structure")
(description "Mantis is a space-efficient data structure that can be
@@ -11480,8 +11221,7 @@ analyses in addition to large-scale sequence-level searches.")
"/bin")))
'("j_count" "b_count" "sjcount")))))))
(inputs
- `(("samtools" ,samtools-0.1)
- ("zlib" ,zlib)))
+ (list samtools-0.1 zlib))
(home-page "https://github.com/pervouchine/sjcount-full/")
(synopsis "Annotation-agnostic splice junction counting pipeline")
(description "Sjcount is a utility for fast quantification of splice
@@ -11556,7 +11296,7 @@ version does count multisplits.")
out ,version))))
#t)))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://lh3.github.io/minimap2/")
(synopsis "Pairwise aligner for genomic and spliced nucleotide sequences")
(description "Minimap2 is a versatile sequence alignment program that
@@ -11587,9 +11327,9 @@ cases include:
"1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq"))))
(build-system python-build-system)
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/lh3/minimap2")
(synopsis "Python binding for minimap2")
(description "This package provides a convenient interface to minimap2,
@@ -11612,7 +11352,7 @@ sequences.")
"04dv5wv8bhsw1imxwyd438bnn9kby7svp44nbcz8lsadzjjci5gs"))))
(build-system gnu-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(arguments
`(#:tests? #f ; There are no tests.
#:phases
@@ -11670,10 +11410,9 @@ Thus the per-base error rate is similar to the raw input reads.")
(install-file "Bandage" (string-append out "/bin"))
#t))))))
(inputs
- `(("qtbase" ,qtbase-5)
- ("qtsvg" ,qtsvg)))
+ (list qtbase-5 qtsvg))
(native-inputs
- `(("imagemagick" ,imagemagick)))
+ (list imagemagick))
(home-page "https://rrwick.github.io/Bandage/")
(synopsis
"Bioinformatics Application for Navigating De novo Assembly Graphs Easily")
@@ -11709,10 +11448,10 @@ contigs alone.")
;; The test suite attempts to execute ../test-driver, which does not exist.
(arguments '(#:tests? #false))
(propagated-inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("gcc" ,gcc-10) ;Code has C++17 requirements
- ("pkg-config" ,pkg-config)))
+ (list gcc-10 ;Code has C++17 requirements
+ pkg-config))
(home-page "https://gitlab.com/german.tischler/libmaus2")
(synopsis "Collection of data structures and algorithms useful for bioinformatics")
(description "libmaus2 is a collection of data structures and
@@ -11753,11 +11492,10 @@ and many lower level support classes.
,#~(list (string-append "--with-libmaus2="
#$(this-package-input "libmaus2")))))
(inputs
- `(("libmaus2" ,libmaus2)
- ("xerces-c" ,xerces-c)))
+ (list libmaus2 xerces-c))
(native-inputs
- `(("gcc" ,gcc-10) ;Code has C++17 requirements
- ("pkg-config" ,pkg-config)))
+ (list gcc-10 ;Code has C++17 requirements
+ pkg-config))
(home-page "https://gitlab.com/german.tischler/biobambam2")
(synopsis "Tools for processing BAM files")
(description "This package contains some tools for processing BAM files
@@ -11798,23 +11536,23 @@ including:
"0jhjn3ilb057hbf6yzrihj13ifxxs32y7nkby8l3lkm28dg4p97h"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationhub" ,r-annotationhub)
- ("r-biomart" ,r-biomart)
- ("r-data-table" ,r-data-table)
- ("r-dbi" ,r-dbi)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-hash" ,r-hash)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rmysql" ,r-rmysql)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-annotationhub
+ r-biomart
+ r-data-table
+ r-dbi
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-hash
+ r-iranges
+ r-rcolorbrewer
+ r-rmysql
+ r-s4vectors
+ r-stringr
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/BIMSBbioinfo/ciRcus")
(synopsis "Annotation, analysis and visualization of circRNA data")
(description "Circus is an R package for annotation, analysis and
@@ -11927,9 +11665,7 @@ conversions, region filtering, FASTA sequence extraction and more.")
"unmapped2anchors.py")))
#t)))))
(inputs
- `(("python2" ,python-2)
- ("python2-pysam" ,python2-pysam)
- ("python2-numpy" ,python2-numpy)))
+ (list python-2 python2-pysam python2-numpy))
(home-page "https://github.com/marvin-jens/find_circ")
(synopsis "circRNA detection from RNA-seq reads")
(description "This package provides tools to detect head-to-tail
@@ -11980,7 +11716,7 @@ in RNA-seq data.")
(string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n")))
(install-file "fast_tsne.R" share)))))))
(inputs
- `(("fftw" ,fftw)))
+ (list fftw))
(home-page "https://github.com/KlugerLab/FIt-SNE")
(synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE")
(description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a
@@ -12078,28 +11814,28 @@ implementation differs in these ways:
" and not test_pca_sparse"
" and not test_pca_reproducible"))))))))
(propagated-inputs
- `(("python-anndata" ,python-anndata)
- ("python-h5py" ,python-h5py)
- ("python-igraph" ,python-igraph)
- ("python-joblib" ,python-joblib)
- ("python-legacy-api-wrap" ,python-legacy-api-wrap)
- ("python-louvain" ,python-louvain-0.6)
- ("python-matplotlib" ,python-matplotlib)
- ("python-natsort" ,python-natsort)
- ("python-networkx" ,python-networkx)
- ("python-numba" ,python-numba)
- ("python-packaging" ,python-packaging)
- ("python-pandas" ,python-pandas)
- ("python-patsy" ,python-patsy)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)
- ("python-seaborn" ,python-seaborn)
- ("python-sinfo" ,python-sinfo)
- ("python-statsmodels" ,python-statsmodels)
- ("python-tables" ,python-tables)
- ("python-pytoml" ,python-pytoml)
- ("python-tqdm" ,python-tqdm)
- ("python-umap-learn" ,python-umap-learn)))
+ (list python-anndata
+ python-h5py
+ python-igraph
+ python-joblib
+ python-legacy-api-wrap
+ python-louvain-0.6
+ python-matplotlib
+ python-natsort
+ python-networkx
+ python-numba
+ python-packaging
+ python-pandas
+ python-patsy
+ python-scikit-learn
+ python-scipy
+ python-seaborn
+ python-sinfo
+ python-statsmodels
+ python-tables
+ python-pytoml
+ python-tqdm
+ python-umap-learn))
(native-inputs
`(;; This package needs anndata.tests, which is not installed.
("python-anndata:source" ,(package-source python-anndata))
@@ -12138,12 +11874,12 @@ million cells.")
(substitute* "setup.py"
(("'sklearn'") "")))))))
(propagated-inputs
- `(("python-annoy" ,python-annoy)
- ("python-cython" ,python-cython)
- ("python-numpy" ,python-numpy)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)
- ("python-umap-learn" ,python-umap-learn)))
+ (list python-annoy
+ python-cython
+ python-numpy
+ python-scikit-learn
+ python-scipy
+ python-umap-learn))
(home-page "https://github.com/Teichlab/bbknn")
(synopsis "Batch balanced KNN")
(description "BBKNN is a batch effect removal tool that can be directly
@@ -12171,14 +11907,14 @@ altering the counts or PCA space.")
"08vk0x6v5c5n7afgd5pcjhsvb424absypxy22hw1cm1n9kirbi77"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-biopython" ,python-biopython)
- ("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-pytest" ,python-pytest)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-seaborn" ,python-seaborn)
- ("python-tqdm" ,python-tqdm)))
+ (list python-biopython
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-pytest
+ python-scikit-learn
+ python-seaborn
+ python-tqdm))
(home-page "https://github.com/MrOlm/drep")
(synopsis "De-replication of microbial genomes assembled from multiple samples")
(description
@@ -12211,24 +11947,24 @@ set.")
(("from job_utils")
"from .job_utils")))))))
(inputs
- `(("python-biopython" ,python-biopython-1.73)
- ("python-boto3" ,python-boto3)
- ("python-h5py" ,python-h5py)
- ("python-lmfit" ,python-lmfit)
- ("python-matplotlib" ,python-matplotlib)
- ("python-networkx" ,python-networkx)
- ("python-numba" ,python-numba)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-psutil" ,python-psutil)
- ("python-pysam" ,python-pysam)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-seaborn" ,python-seaborn)
- ("python-tqdm" ,python-tqdm)
- ;; drep is needed for deprecated plot utilities
- ("python-drep" ,python-drep)))
- (native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-biopython-1.73
+ python-boto3
+ python-h5py
+ python-lmfit
+ python-matplotlib
+ python-networkx
+ python-numba
+ python-numpy
+ python-pandas
+ python-psutil
+ python-pysam
+ python-scikit-learn
+ python-seaborn
+ python-tqdm
+ ;; drep is needed for deprecated plot utilities
+ python-drep))
+ (native-inputs
+ (list python-pytest))
(home-page "https://github.com/MrOlm/inStrain")
(synopsis "Calculation of strain-level metrics")
(description
@@ -12359,9 +12095,9 @@ allowing the insertion of arbitrary types into the tree.")
(setenv "PY_IGNORE_IMPORTMISMATCH" "1")
#t)))))
(propagated-inputs
- `(("python-sortedcontainers" ,python-sortedcontainers)))
+ (list python-sortedcontainers))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-pytest))
(home-page "https://github.com/chaimleib/intervaltree")
(synopsis "Editable interval tree data structure")
(description
@@ -12401,7 +12137,7 @@ bound.")
"/bin"))
#t)))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/4dn-dcic/pairix")
(synopsis "Support for querying pairix-indexed bgzipped text files")
(description
@@ -12422,7 +12158,7 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
"038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-six" ,python-six)))
+ (list python-six))
(home-page "http://mattshirley.com")
(synopsis "Random access to fasta subsequences")
(description
@@ -12470,29 +12206,26 @@ fasta subsequences.")
(when tests?
(invoke "python" "-m" "pytest" "-v")))))))
(propagated-inputs
- `(("python-asciitree" ,python-asciitree)
- ("python-biopython" ,python-biopython)
- ("python-click" ,python-click)
- ("python-cytoolz" ,python-cytoolz-for-cooler)
- ("python-dask" ,python-dask)
- ("python-h5py" ,python-h5py)
- ("python-multiprocess" ,python-multiprocess)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-pyfaidx" ,python-pyfaidx)
- ("python-pypairix" ,python-pypairix)
- ("python-pysam" ,python-pysam)
- ("python-pyyaml" ,python-pyyaml)
- ("python-scipy" ,python-scipy)
- ("python-simplejson" ,python-simplejson)
- ("python-six" ,python-six)
- ("python-sparse" ,python-sparse)))
- (native-inputs
- `(("python-codecov" ,python-codecov)
- ("python-mock" ,python-mock)
- ("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-pytest-flake8" ,python-pytest-flake8)))
+ (list python-asciitree
+ python-biopython
+ python-click
+ python-cytoolz-for-cooler
+ python-dask
+ python-h5py
+ python-multiprocess
+ python-numpy
+ python-pandas
+ python-pyfaidx
+ python-pypairix
+ python-pysam
+ python-pyyaml
+ python-scipy
+ python-simplejson
+ python-six
+ python-sparse))
+ (native-inputs
+ (list python-codecov python-mock python-pytest python-pytest-cov
+ python-pytest-flake8))
;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
(home-page "https://github.com/open2c/cooler")
(synopsis "Sparse binary format for genomic interaction matrices")
@@ -12526,14 +12259,14 @@ such as Hi-C contact matrices.")
(when tests?
(invoke "python" "-m" "pytest" "-v")))))))
(propagated-inputs
- `(("python-cooler" ,python-cooler)
- ("python-intervaltree" ,python-intervaltree)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-scipy" ,python-scipy)
- ("python-tables" ,python-tables)))
- (native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-cooler
+ python-intervaltree
+ python-numpy
+ python-pandas
+ python-scipy
+ python-tables))
+ (native-inputs
+ (list python-pytest))
(home-page "https://github.com/deeptools/HiCMatrix/")
(synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks")
(description
@@ -12566,21 +12299,21 @@ the HiCExplorer and pyGenomeTracks packages.")
(("==") ">="))
#t)))))
(propagated-inputs
- `(("python-biopython" ,python-biopython)
- ("python-configparser" ,python-configparser)
- ("python-cooler" ,python-cooler)
- ("python-future" ,python-future)
- ("python-intervaltree" ,python-intervaltree)
- ("python-jinja2" ,python-jinja2)
- ("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-pybigwig" ,python-pybigwig)
- ("python-pysam" ,python-pysam)
- ("python-scipy" ,python-scipy)
- ("python-six" ,python-six)
- ("python-tables" ,python-tables)
- ("python-unidecode" ,python-unidecode)))
+ (list python-biopython
+ python-configparser
+ python-cooler
+ python-future
+ python-intervaltree
+ python-jinja2
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-pybigwig
+ python-pysam
+ python-scipy
+ python-six
+ python-tables
+ python-unidecode))
(home-page "https://hicexplorer.readthedocs.io")
(synopsis "Process, analyze and visualize Hi-C data")
(description
@@ -12617,17 +12350,17 @@ genomic scores), long range contacts and the visualization of viewpoints.")
"matplotlib >=3.1.1"))
#t)))))
(propagated-inputs
- `(("python-future" ,python-future)
- ("python-gffutils" ,python-gffutils)
- ("python-hicmatrix" ,python-hicmatrix)
- ("python-intervaltree" ,python-intervaltree)
- ("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)
- ("python-pybigwig" ,python-pybigwig)
- ("python-pysam" ,python-pysam)
- ("python-tqdm" ,python-tqdm)))
- (native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-future
+ python-gffutils
+ python-hicmatrix
+ python-intervaltree
+ python-matplotlib
+ python-numpy
+ python-pybigwig
+ python-pysam
+ python-tqdm))
+ (native-inputs
+ (list python-pytest))
(home-page "https://pygenometracks.readthedocs.io")
(synopsis "Program and library to plot beautiful genome browser tracks")
(description
@@ -12651,10 +12384,7 @@ pyGenomeTracks can make plots with or without Hi-C data.")
(build-system python-build-system)
(arguments `(#:tests? #false)) ; there are none
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-scipy" ,python-scipy)
- ("python-scikit-learn" ,python-scikit-learn)))
+ (list python-numpy python-pandas python-scipy python-scikit-learn))
(home-page "https://github.com/hiclib/iced")
(synopsis "ICE normalization")
(description "This is a package for normalizing Hi-C contact counts
@@ -12688,11 +12418,8 @@ efficiently.")
(list "test_data/hic2cool_0.4.2_single_res.cool"
"test_data/hic2cool_0.7.0_multi_res.mcool")))))))
(propagated-inputs
- `(("python-cooler" ,python-cooler)
- ("python-h5py" ,python-h5py)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-scipy" ,python-scipy)))
+ (list python-cooler python-h5py python-numpy python-pandas
+ python-scipy))
(home-page "https://github.com/4dn-dcic/hic2cool")
(synopsis "Converter for .hic and .cool files")
(description
@@ -12717,11 +12444,7 @@ matrices.")
(properties `((upstream-name . "poRe")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bit64" ,r-bit64)
- ("r-data-table" ,r-data-table)
- ("r-rhdf5" ,r-rhdf5)
- ("r-shiny" ,r-shiny)
- ("r-svdialogs" ,r-svdialogs)))
+ (list r-bit64 r-data-table r-rhdf5 r-shiny r-svdialogs))
(home-page "https://sourceforge.net/projects/rpore/")
(synopsis "Visualize Nanopore sequencing data")
(description
@@ -12748,15 +12471,15 @@ sequencing data.")
"0w8bsq5myiwkfhh83nm6is5ichiyvwa1axx2szvxnzq39x6knf66"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-assertthat" ,r-assertthat)
- ("r-biobase" ,r-biobase)
- ("r-biocmanager" ,r-biocmanager)
- ("r-digest" ,r-digest)
- ("r-pkgmaker" ,r-pkgmaker)
- ("r-plyr" ,r-plyr)
- ("r-reshape2" ,r-reshape2)
- ("r-stringr" ,r-stringr)))
+ (list r-annotationdbi
+ r-assertthat
+ r-biobase
+ r-biocmanager
+ r-digest
+ r-pkgmaker
+ r-plyr
+ r-reshape2
+ r-stringr))
(home-page "https://github.com/renozao/xbioc/")
(synopsis "Extra base functions for Bioconductor")
(description "This package provides extra utility functions to perform
@@ -12781,12 +12504,12 @@ provided by Bioconductor packages.")
"128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-formula" ,r-formula)
- ("r-ggplot2" ,r-ggplot2)
- ("r-pkgmaker" ,r-pkgmaker)
- ("r-plyr" ,r-plyr)
- ("r-rngtools" ,r-rngtools)
- ("r-scales" ,r-scales)))
+ (list r-formula
+ r-ggplot2
+ r-pkgmaker
+ r-plyr
+ r-rngtools
+ r-scales))
(home-page "https://github.com/shenorrLab/csSAM/")
(synopsis "Cell type-specific statistical analysis of microarray")
(description "This package implements the method csSAM that computes
@@ -12812,23 +12535,23 @@ SAM.")
"1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-abind" ,r-abind)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-cssam" ,r-cssam)
- ("r-dplyr" ,r-dplyr)
- ("r-e1071" ,r-e1071)
- ("r-edger" ,r-edger)
- ("r-ggplot2" ,r-ggplot2)
- ("r-nmf" ,r-nmf)
- ("r-openxlsx" ,r-openxlsx)
- ("r-pkgmaker" ,r-pkgmaker)
- ("r-plyr" ,r-plyr)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-rngtools" ,r-rngtools)
- ("r-scales" ,r-scales)
- ("r-stringr" ,r-stringr)
- ("r-xbioc" ,r-xbioc)))
+ (list r-abind
+ r-annotationdbi
+ r-biobase
+ r-cssam
+ r-dplyr
+ r-e1071
+ r-edger
+ r-ggplot2
+ r-nmf
+ r-openxlsx
+ r-pkgmaker
+ r-plyr
+ r-preprocesscore
+ r-rngtools
+ r-scales
+ r-stringr
+ r-xbioc))
(home-page "https://github.com/shenorrLab/bseqsc")
(synopsis "Deconvolution of bulk sequencing experiments using single cell data")
(description "BSeq-sc is a bioinformatics analysis pipeline that
@@ -12892,13 +12615,10 @@ Barcoding Kit or Rapid Barcoding Kit.")
;; requires python >=2.7, <3.0, and the same for python dependencies
(arguments `(#:python ,python-2))
(inputs
- `(("hdf5" ,hdf5)))
+ (list hdf5))
(propagated-inputs
- `(("python-dateutil" ,python2-dateutil)
- ("python-h5py" ,python2-h5py)
- ("python-matplotlib" ,python2-matplotlib)
- ("python-pandas" ,python2-pandas)
- ("python-seaborn" ,python2-seaborn)))
+ (list python2-dateutil python2-h5py python2-matplotlib
+ python2-pandas python2-seaborn))
(home-page "https://poretools.readthedocs.io")
(synopsis "Toolkit for working with nanopore sequencing data")
(description
@@ -12966,14 +12686,14 @@ of the Hierarchical Data Format (HDF5) standard.")
(list "JAMM.sh" "SignalGenerator.sh")))
#t)))))
(inputs
- `(("bash" ,bash)
- ("coreutils" ,coreutils)
- ("gawk" ,gawk)
- ("perl" ,perl)
- ("r-minimal" ,r-minimal)
- ;;("r-parallel" ,r-parallel)
- ("r-signal" ,r-signal)
- ("r-mclust" ,r-mclust)))
+ (list bash
+ coreutils
+ gawk
+ perl
+ r-minimal
+ ;;("r-parallel" ,r-parallel)
+ r-signal
+ r-mclust))
(home-page "https://github.com/mahmoudibrahim/JAMM")
(synopsis "Peak finder for NGS datasets")
(description
@@ -13038,63 +12758,59 @@ datasets.")
(string-append bin "ngless-" ,version "-bwa"))
#t))))))
(inputs
- `(("prodigal" ,prodigal)
- ("bwa" ,bwa)
- ("samtools" ,samtools)
- ("minimap2" ,minimap2)
- ("ghc-aeson" ,ghc-aeson)
- ("ghc-ansi-terminal" ,ghc-ansi-terminal)
- ("ghc-async" ,ghc-async)
- ("ghc-atomic-write" ,ghc-atomic-write)
- ("ghc-bytestring-lexing" ,ghc-bytestring-lexing)
- ("ghc-conduit" ,ghc-conduit)
- ("ghc-conduit-algorithms" ,ghc-conduit-algorithms)
- ("ghc-conduit-extra" ,ghc-conduit-extra)
- ("ghc-configurator" ,ghc-configurator)
- ("ghc-convertible" ,ghc-convertible)
- ("ghc-data-default" ,ghc-data-default)
- ("ghc-diagrams-core" ,ghc-diagrams-core)
- ("ghc-diagrams-lib" ,ghc-diagrams-lib)
- ("ghc-diagrams-svg" ,ghc-diagrams-svg)
- ("ghc-double-conversion" ,ghc-double-conversion)
- ("ghc-edit-distance" ,ghc-edit-distance)
- ("ghc-either" ,ghc-either)
- ("ghc-errors" ,ghc-errors)
- ("ghc-extra" ,ghc-extra)
- ("ghc-filemanip" ,ghc-filemanip)
- ("ghc-file-embed" ,ghc-file-embed)
- ("ghc-gitrev" ,ghc-gitrev)
- ("ghc-hashtables" ,ghc-hashtables)
- ("ghc-http-conduit" ,ghc-http-conduit)
- ("ghc-inline-c" ,ghc-inline-c)
- ("ghc-inline-c-cpp" ,ghc-inline-c-cpp)
- ("ghc-int-interval-map" ,ghc-int-interval-map)
- ("ghc-missingh" ,ghc-missingh)
- ("ghc-optparse-applicative" ,ghc-optparse-applicative)
- ("ghc-regex" ,ghc-regex)
- ("ghc-safe" ,ghc-safe)
- ("ghc-safeio" ,ghc-safeio)
- ("ghc-strict" ,ghc-strict)
- ("ghc-tar" ,ghc-tar)
- ("ghc-tar-conduit" ,ghc-tar-conduit)
- ("ghc-unliftio" ,ghc-unliftio)
- ("ghc-unliftio-core" ,ghc-unliftio-core)
- ("ghc-vector" ,ghc-vector)
- ("ghc-yaml" ,ghc-yaml)
- ("ghc-zlib" ,ghc-zlib)))
+ (list prodigal
+ bwa
+ samtools
+ minimap2
+ ghc-aeson
+ ghc-ansi-terminal
+ ghc-async
+ ghc-atomic-write
+ ghc-bytestring-lexing
+ ghc-conduit
+ ghc-conduit-algorithms
+ ghc-conduit-extra
+ ghc-configurator
+ ghc-convertible
+ ghc-data-default
+ ghc-diagrams-core
+ ghc-diagrams-lib
+ ghc-diagrams-svg
+ ghc-double-conversion
+ ghc-edit-distance
+ ghc-either
+ ghc-errors
+ ghc-extra
+ ghc-filemanip
+ ghc-file-embed
+ ghc-gitrev
+ ghc-hashtables
+ ghc-http-conduit
+ ghc-inline-c
+ ghc-inline-c-cpp
+ ghc-int-interval-map
+ ghc-missingh
+ ghc-optparse-applicative
+ ghc-regex
+ ghc-safe
+ ghc-safeio
+ ghc-strict
+ ghc-tar
+ ghc-tar-conduit
+ ghc-unliftio
+ ghc-unliftio-core
+ ghc-vector
+ ghc-yaml
+ ghc-zlib))
(propagated-inputs
- `(("r-r6" ,r-r6)
- ("r-hdf5r" ,r-hdf5r)
- ("r-iterators" ,r-iterators)
- ("r-itertools" ,r-itertools)
- ("r-matrix" ,r-matrix)))
- (native-inputs
- `(("ghc-hpack" ,ghc-hpack)
- ("ghc-quickcheck" ,ghc-quickcheck)
- ("ghc-test-framework" ,ghc-test-framework)
- ("ghc-test-framework-hunit",ghc-test-framework-hunit)
- ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
- ("ghc-test-framework-th" ,ghc-test-framework-th)))
+ (list r-r6 r-hdf5r r-iterators r-itertools r-matrix))
+ (native-inputs
+ (list ghc-hpack
+ ghc-quickcheck
+ ghc-test-framework
+ ghc-test-framework-hunit
+ ghc-test-framework-quickcheck2
+ ghc-test-framework-th))
(home-page "https://ngless.embl.de/")
(synopsis "DSL for processing next-generation sequencing data")
(description "Ngless is a domain-specific language for
@@ -13117,17 +12833,14 @@ datasets.")
(sha256 (base32 "0fd728b5if89vj5j4f9y7k0b2xv2ycz5a21iy15wbdcf5bhim7i8"))))
(build-system haskell-build-system)
(inputs
- `(("ghc-either" ,ghc-either)
- ("ghc-primitive" ,ghc-primitive)
- ("ghc-vector" ,ghc-vector)
- ("ghc-vector-algorithms" ,ghc-vector-algorithms)))
+ (list ghc-either ghc-primitive ghc-vector ghc-vector-algorithms))
(native-inputs
- `(("ghc-hedgehog" ,ghc-hedgehog)
- ("ghc-tasty" ,ghc-tasty)
- ("ghc-tasty-hedgehog" ,ghc-tasty-hedgehog)
- ("ghc-tasty-hunit" ,ghc-tasty-hunit)
- ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
- ("ghc-tasty-th" ,ghc-tasty-th)))
+ (list ghc-hedgehog
+ ghc-tasty
+ ghc-tasty-hedgehog
+ ghc-tasty-hunit
+ ghc-tasty-quickcheck
+ ghc-tasty-th))
(home-page "https://github.com/luispedro/interval-to-int#readme")
(synopsis "Interval map structure in Haskell")
(description "An interval map structure that is optimized for low
@@ -13300,17 +13013,17 @@ polymorphisms) and indels with respect to a reference genome and more.")
(base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-biopython" ,python-biopython)
- ("python-future" ,python-future)
- ("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)
- ("python-reportlab" ,python-reportlab)
- ("python-pandas" ,python-pandas)
- ("python-pysam" ,python-pysam)
- ("python-pyfaidx" ,python-pyfaidx)
- ("python-scipy" ,python-scipy)
- ;; R packages
- ("r-dnacopy" ,r-dnacopy)))
+ (list python-biopython
+ python-future
+ python-matplotlib
+ python-numpy
+ python-reportlab
+ python-pandas
+ python-pysam
+ python-pyfaidx
+ python-scipy
+ ;; R packages
+ r-dnacopy))
(home-page "https://cnvkit.readthedocs.org/")
(synopsis "Copy number variant detection from targeted DNA sequencing")
(description
@@ -13337,11 +13050,11 @@ Torrent.")
(build-system python-build-system)
(arguments '(#:tests? #false)) ; there are none
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(inputs
- `(("fftw" ,fftw)))
+ (list fftw))
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
(home-page "https://github.com/KlugerLab/pyFIt-SNE")
(synopsis "FFT-accelerated Interpolation-based t-SNE")
(description
@@ -13410,10 +13123,8 @@ is a Cython wrapper for FIt-SNE.")
#t)))
#:jdk ,openjdk11))
(inputs
- `(("gawk" ,gawk)
- ("java-eclipse-jdt-core" ,java-eclipse-jdt-core)
- ("java-eclipse-jdt-compiler-apt" ,java-eclipse-jdt-compiler-apt)
- ("java-openmpi" ,java-openmpi)))
+ (list gawk java-eclipse-jdt-core java-eclipse-jdt-compiler-apt
+ java-openmpi))
(home-page "https://sourceforge.net/projects/bbmap/")
(synopsis "Aligner and other tools for short sequencing reads")
(description
@@ -13468,8 +13179,7 @@ to an artifact/contaminant file.")
(install-file "Manual.pdf" doc)
(install-file "Columbus_manual.pdf" doc)))))))
(inputs
- `(("openmpi" ,openmpi)
- ("zlib" ,zlib)))
+ (list openmpi zlib))
(native-inputs
`(("texlive" ,(texlive-updmap.cfg (list texlive-latex-graphics
texlive-fonts-ec
@@ -13501,19 +13211,19 @@ repeated areas between contigs.")
'(for-each delete-file (find-files "." "\\.c")))))
(build-system python-build-system)
(native-inputs
- `(("python-joblib" ,python-joblib)))
+ (list python-joblib))
(propagated-inputs
- `(("python-click" ,python-click)
- ("python-cython" ,python-cython)
- ("python-h5py" ,python-h5py)
- ("python-loompy" ,python-loompy)
- ("python-matplotlib" ,python-matplotlib)
- ("python-numba" ,python-numba)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-pysam" ,python-pysam)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)))
+ (list python-click
+ python-cython
+ python-h5py
+ python-loompy
+ python-matplotlib
+ python-numba
+ python-numpy
+ python-pandas
+ python-pysam
+ python-scikit-learn
+ python-scipy))
(home-page "https://github.com/velocyto-team/velocyto.py")
(synopsis "RNA velocity analysis for single cell RNA-seq data")
(description
@@ -13565,14 +13275,14 @@ includes a command line tool and an analysis pipeline.")
`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
#t)))))
(inputs
- `(("htslib" ,htslib)
- ("r-minimal" ,r-minimal)
- ("r-circlize" ,r-circlize)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("samtools" ,samtools)
- ("star" ,star)
- ("zlib" ,zlib)))
+ (list htslib
+ r-minimal
+ r-circlize
+ r-genomicalignments
+ r-genomicranges
+ samtools
+ star
+ zlib))
(home-page "https://github.com/suhrig/arriba")
(synopsis "Gene fusion detection from RNA-Seq data ")
(description
@@ -13611,7 +13321,7 @@ tools which build on STAR, Arriba does not require to reduce the
(modify-phases %standard-phases
(delete 'configure))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://adapterremoval.readthedocs.io/")
(synopsis "Rapid sequence adapter trimming, identification, and read merging")
(description
@@ -13730,7 +13440,7 @@ let before_space s =
("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
("pkg-config" ,pkg-config)))
(propagated-inputs
- `(("pplacer-scripts" ,pplacer-scripts)))
+ (list pplacer-scripts))
(synopsis "Phylogenetic placement of biological sequences")
(description
"Pplacer places query sequences on a fixed reference phylogenetic tree
@@ -13800,11 +13510,8 @@ downstream analysis.")
(lambda _
(setenv "HOME" "/tmp"))))))
(inputs
- `(("python-dendropy" ,python-dendropy)
- ("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)
- ("python-pysam" ,python-pysam)
- ("python-scipy" ,python-scipy)))
+ (list python-dendropy python-matplotlib python-numpy python-pysam
+ python-scipy))
(home-page "https://ecogenomics.github.io/CheckM/")
(synopsis "Assess the quality of putative genome bins")
(description
@@ -13836,14 +13543,14 @@ proximity within a reference genome.")
"08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
(build-system python-build-system)
(inputs
- `(("python-pandas" ,python-pandas)
- ("python-future" ,python-future)
- ("python-scipy" ,python-scipy)
- ("python-matplotlib" ,python-matplotlib)
- ("python-regex" ,python-regex)
- ("python-pysam" ,python-pysam)))
+ (list python-pandas
+ python-future
+ python-scipy
+ python-matplotlib
+ python-regex
+ python-pysam))
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
(home-page "https://github.com/CGATOxford/UMI-tools")
(synopsis "Tools for analyzing unique modular identifiers")
(description "This package provides tools for dealing with @dfn{Unique
@@ -13883,12 +13590,9 @@ on the needs of the user.")
(modify-phases %standard-phases
(delete 'configure))))
(inputs
- `(("boost" ,boost)
- ("htslib" ,htslib)
- ("ncurses" ,ncurses)
- ("zlib" ,zlib)))
+ (list boost htslib ncurses zlib))
(native-inputs
- `(("lcov" ,lcov)))
+ (list lcov))
(home-page "https://github.com/ParkerLab/ataqv")
(synopsis "Toolkit for quality control and visualization of ATAC-seq data")
(description "This package provides a toolkit for measuring and comparing
@@ -13912,13 +13616,13 @@ might be caused by ATAC-seq library prep or sequencing. The main program,
(base32 "08438h16cfry5kqh3y9hs8q1b1a8bxhblsm75knviz5r6q0n1jxh"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-mass" ,r-mass)
- ("r-dplyr" ,r-dplyr)
- ("r-tidyr" ,r-tidyr)
- ("r-purrr" ,r-purrr)
- ("r-readr" ,r-readr)
- ("r-magrittr" ,r-magrittr)
- ("r-ggplot2" ,r-ggplot2)))
+ (list r-mass
+ r-dplyr
+ r-tidyr
+ r-purrr
+ r-readr
+ r-magrittr
+ r-ggplot2))
(home-page "https://github.com/kcha/psiplot")
(synopsis "Plot percent spliced-in values of alternatively-spliced exons")
(description
@@ -13952,10 +13656,10 @@ are generated using @code{ggplot2}.")
;; disable building them.
"-DENABLE_PYTHON=OFF")))
(inputs
- `(;("hdf5" ,hdf5-1.10)
- ("zstd" ,zstd "lib")))
+ (list ;("hdf5" ,hdf5-1.10)
+ `(,zstd "lib")))
(native-inputs
- `(("googlebenchmark" ,googlebenchmark)))
+ (list googlebenchmark))
(home-page "https://github.com/nanoporetech/vbz_compression/")
(synopsis "VBZ compression plugin for nanopore signal data")
(description
@@ -13994,12 +13698,9 @@ effective when applied to the signal dataset.")
"/hdf5/lib/plugin/libvbz_hdf_plugin.so")
"ont_fast5_api/vbz_plugin/"))))))
(inputs
- `(("vbz-compression" ,vbz-compression)))
+ (list vbz-compression))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
- ("python-h5py" ,python-h5py)
- ("python-packaging" ,python-packaging)
- ("python-progressbar33" ,python-progressbar33)))
+ (list python-numpy python-h5py python-packaging python-progressbar33))
(home-page "https://github.com/nanoporetech/ont_fast5_api")
(synopsis "Interface to HDF5 files of the Oxford Nanopore fast5 file format")
(description
@@ -14035,13 +13736,13 @@ and reflect the fast5 file schema, and tools to convert between
(substitute* "setup.py"
((", <3.0") ""))))))) ; matplotlib
(inputs
- `(("python-matplotlib" ,python-matplotlib)
- ("python-networkx" ,python-networkx)
- ("python-numpy" ,python-numpy)
- ("python-pybigwig" ,python-pybigwig)
- ("python-biopython" ,python-biopython-1.73)
- ("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)))
+ (list python-matplotlib
+ python-networkx
+ python-numpy
+ python-pybigwig
+ python-biopython-1.73
+ python-scikit-learn
+ python-scipy))
(home-page "https://github.com/phoenixding/tbsp/")
(synopsis "SNP-based trajectory inference")
(description
@@ -14072,8 +13773,7 @@ mutations from scRNA-Seq data.")
(delete-file-recursively "htslib") #t))))
(build-system gnu-build-system)
(inputs
- `(("htslib" ,htslib)
- ("zlib" ,zlib)))
+ (list htslib zlib))
(arguments
`(#:tests? #f ; There are no tests to run.
#:phases
@@ -14249,7 +13949,7 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "fsom" bin)))))))
(native-inputs
- `(("gcc" ,gcc-6)))
+ (list gcc-6))
(home-page "https://github.com/ekg/fsom")
(synopsis "Manage SOM (Self-Organizing Maps) neural networks")
(description "A tiny C library for managing SOM (Self-Organizing Maps)
@@ -14360,15 +14060,15 @@ library automatically handles index file generation and use.")
#t))))
(build-system cmake-build-system)
(inputs
- `(("bzip2" ,bzip2)
- ("htslib" ,htslib)
- ("fastahack" ,fastahack)
- ("perl" ,perl)
- ("python" ,python)
- ("smithwaterman" ,smithwaterman)
- ("tabixpp" ,tabixpp)
- ("xz" ,xz)
- ("zlib" ,zlib)))
+ (list bzip2
+ htslib
+ fastahack
+ perl
+ python
+ smithwaterman
+ tabixpp
+ xz
+ zlib))
(native-inputs
`(("pkg-config" ,pkg-config)
;; Submodules.
@@ -14453,11 +14153,7 @@ manipulations on VCF files.")
#t))))
(build-system meson-build-system)
(inputs
- `(("fastahack" ,fastahack)
- ("htslib" ,htslib)
- ("smithwaterman" ,smithwaterman)
- ("tabixpp" ,tabixpp)
- ("vcflib" ,vcflib)))
+ (list fastahack htslib smithwaterman tabixpp vcflib))
(native-inputs
`(("bash-tap" ,bash-tap)
("bc" ,bc)
@@ -14574,24 +14270,24 @@ pairs.")
"16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n"))))
(build-system r-build-system)
(inputs
- `(("boost" ,boost)))
+ (list boost))
(propagated-inputs
- `(("r-hdf5r" ,r-hdf5r)
- ("r-mass" ,r-mass)
- ("r-mgcv" ,r-mgcv)
- ("r-pcamethods" ,r-pcamethods)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ;; Suggested packages
- ("r-rtsne" ,r-rtsne)
- ("r-cluster" ,r-cluster)
- ("r-abind" ,r-abind)
- ("r-h5" ,r-h5)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-rsamtools" ,r-rsamtools)
- ("r-edger" ,r-edger)
- ("r-igraph" ,r-igraph)))
+ (list r-hdf5r
+ r-mass
+ r-mgcv
+ r-pcamethods
+ r-rcpp
+ r-rcpparmadillo
+ ;; Suggested packages
+ r-rtsne
+ r-cluster
+ r-abind
+ r-h5
+ r-biocgenerics
+ r-genomicalignments
+ r-rsamtools
+ r-edger
+ r-igraph))
(home-page "https://velocyto.org")
(synopsis "RNA velocity estimation in R")
(description
@@ -14629,10 +14325,8 @@ patterns.")
(("install MethylDackel \\$\\(prefix\\)" match)
(string-append "install -d $(prefix); " match))))))))
(inputs
- `(("curl" ,curl) ; XXX: needed by libbigwig
- ("htslib" ,htslib-1.9)
- ("libbigwig" ,libbigwig)
- ("zlib" ,zlib)))
+ (list curl ; XXX: needed by libbigwig
+ htslib-1.9 libbigwig zlib))
;; Needed for tests
(native-inputs
`(("python" ,python-wrapper)))
@@ -14702,9 +14396,9 @@ containing the reference genome as well.")
;; unknown reasons.
(invoke "make" "-C" "test" "msa_view"))))))
(inputs
- `(("clapack" ,clapack)))
+ (list clapack))
(native-inputs
- `(("perl" ,perl)))
+ (list perl))
(home-page "http://compgen.cshl.edu/phast/")
(synopsis "Phylogenetic analysis with space/time models")
(description
@@ -14749,15 +14443,15 @@ alignments, trees and genomic annotations.")
(find-files "." "\\.gz"))
#t)))))
(propagated-inputs
- `(("python-argcomplete" ,python-argcomplete)
- ("python-argh" ,python-argh)
- ("python-biopython" ,python-biopython)
- ("python-pybedtools" ,python-pybedtools)
- ("python-pyfaidx" ,python-pyfaidx)
- ("python-simplejson" ,python-simplejson)
- ("python-six" ,python-six)))
+ (list python-argcomplete
+ python-argh
+ python-biopython
+ python-pybedtools
+ python-pyfaidx
+ python-simplejson
+ python-six))
(native-inputs
- `(("python-nose" , python-nose)))
+ (list python-nose))
(home-page "https://github.com/daler/gffutils")
(synopsis "Tool for manipulation of GFF and GTF files")
(description
@@ -14790,7 +14484,7 @@ than is possible with plain-text methods alone.")
`(("java-commons-lang2" ,java-commons-lang)
("java-args4j" ,java-args4j)))
(native-inputs
- `(("java-junit" ,java-junit)))
+ (list java-junit))
(home-page "https://github.com/cbg-ethz/InDelFixer/")
(synopsis "Iterative and sensitive NGS sequence aligner")
(description "InDelFixer is a sensitive aligner for 454, Illumina and
@@ -14827,10 +14521,9 @@ The output is in SAM format.")
#$(this-package-input "libxml2")
"/include/libxml2"))))
(propagated-inputs
- `(("libxml2" ,libxml2)))
+ (list libxml2))
(native-inputs
- `(("check" ,check-0.14)
- ("swig" ,swig)))
+ (list check-0.14 swig))
(home-page "http://sbml.org/Software/libSBML")
(synopsis "Process SBML files and data streams")
(description "LibSBML is a library to help you read, write, manipulate,
@@ -14915,12 +14608,12 @@ international community.")
(install-file script bin))
scripts)))))))))
(inputs
- `(("gzip" ,gzip)
- ("perl" ,perl)
- ("rsync" ,rsync)
- ("sed" ,sed)
- ("wget" ,wget)
- ("which" ,which)))
+ (list gzip
+ perl
+ rsync
+ sed
+ wget
+ which))
(home-page "https://github.com/DerrickWood/kraken2")
(synopsis "Taxonomic sequence classification system")
(description "Kraken is a taxonomic sequence classifier that assigns
@@ -14952,9 +14645,7 @@ genomes known to contain a given k-mer.")
("python" ,python-wrapper)
("zlib" ,zlib)))
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("which" ,which)))
+ (list autoconf automake which))
(home-page "https://csb5.github.io/lofreq/")
(synopsis "Sensitive variant calling from sequencing data ")
(description "LoFreq is a fast and sensitive variant-caller for inferring
@@ -14980,11 +14671,9 @@ usually ignored by other methods or only used for filtering.")
(build-system gnu-build-system)
(arguments `(#:parallel-tests? #false)) ; not supported
(inputs
- `(("htslib" ,htslib)
- ("zlib" ,zlib)))
+ (list htslib zlib))
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)))
+ (list autoconf automake))
(home-page "https://andersen-lab.github.io/ivar/html/")
(synopsis "Tools for amplicon-based sequencing")
(description "iVar is a computational package that contains functions
@@ -15008,7 +14697,7 @@ broadly useful for viral amplicon-based sequencing. ")
(build-system python-build-system)
(arguments `(#:tests? #false)) ; the tests access the web
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-pytest))
(home-page "https://github.com/konstantint/pyliftover")
(synopsis "Python implementation of UCSC liftOver genome coordinate conversion")
(description
@@ -15055,15 +14744,15 @@ coordinates between different assemblies.")
("hostname" ,inetutils)
("openssl" ,openssl)))
(inputs
- `(("time" ,time)))
+ (list time))
(propagated-inputs
- `(("python-apsw" ,python-apsw)
- ("python-gevent" ,python-gevent)
- ("python-pandas" ,python-pandas)
- ("python-paramiko" ,python-paramiko)
- ("python-pyyaml" ,python-pyyaml)
- ("python-ruffus" ,python-ruffus)
- ("python-sqlalchemy" ,python-sqlalchemy)))
+ (list python-apsw
+ python-gevent
+ python-pandas
+ python-paramiko
+ python-pyyaml
+ python-ruffus
+ python-sqlalchemy))
(home-page "https://github.com/cgat-developers/cgat-core")
(synopsis "Computational genomics analysis toolkit")
(description
@@ -15159,7 +14848,7 @@ large-scale data-analysis.")
("python-scikit-learn" ,python-scikit-learn)
("r-minimal" ,r-minimal)))
(native-inputs
- `(("perl-module-build" ,perl-module-build)))
+ (list perl-module-build))
(home-page "https://github.com/dekkerlab/cworld-dekker")
(synopsis "Utility and analysis scripts for 3C, 4C, 5C, and Hi-C data")
(description "This package is a collection of Perl, Python, and R
@@ -15275,16 +14964,16 @@ my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ && /\\.t$/} readdir
runtests(@test_files);
"))))))))
(inputs
- `(("bioperl-minimal" ,bioperl-minimal)
- ("perl-bio-db-hts" ,perl-bio-db-hts)
- ("perl-dbi" ,perl-dbi)
- ("perl-dbd-mysql" ,perl-dbd-mysql)
- ("perl-libwww" ,perl-libwww)
- ("perl-http-tiny" ,perl-http-tiny)
- ("perl-json" ,perl-json)
- ("which" ,which)))
+ (list bioperl-minimal
+ perl-bio-db-hts
+ perl-dbi
+ perl-dbd-mysql
+ perl-libwww
+ perl-http-tiny
+ perl-json
+ which))
(propagated-inputs
- `(("kentutils" ,kentutils)))
+ (list kentutils))
(native-inputs
`(("unzip" ,unzip)
("perl" ,perl)
@@ -15330,39 +15019,39 @@ translates between different variant encodings.")
"1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb"))))
(properties `((upstream-name . "Signac")))
(build-system r-build-system)
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
(propagated-inputs
- `(("r-annotationfilter" ,r-annotationfilter)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-biovizbase" ,r-biovizbase)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-fastmatch" ,r-fastmatch)
- ("r-future" ,r-future)
- ("r-future-apply" ,r-future-apply)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbio" ,r-ggbio)
- ("r-ggforce" ,r-ggforce)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-ggseqlogo" ,r-ggseqlogo)
- ("r-iranges" ,r-iranges)
- ("r-irlba" ,r-irlba)
- ("r-lsa" ,r-lsa)
- ("r-matrix" ,r-matrix)
- ("r-patchwork" ,r-patchwork)
- ("r-pbapply" ,r-pbapply)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpproll" ,r-rcpproll)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-seurat" ,r-seurat)
- ("r-seuratobject" ,r-seuratobject)
- ("r-stringi" ,r-stringi)
- ("r-tidyr" ,r-tidyr)))
+ (list r-annotationfilter
+ r-biocgenerics
+ r-biostrings
+ r-biovizbase
+ r-data-table
+ r-dplyr
+ r-fastmatch
+ r-future
+ r-future-apply
+ r-genomeinfodb
+ r-genomicranges
+ r-ggbio
+ r-ggforce
+ r-ggplot2
+ r-ggrepel
+ r-ggseqlogo
+ r-iranges
+ r-irlba
+ r-lsa
+ r-matrix
+ r-patchwork
+ r-pbapply
+ r-rcpp
+ r-rcpproll
+ r-rsamtools
+ r-s4vectors
+ r-scales
+ r-seurat
+ r-seuratobject
+ r-stringi
+ r-tidyr))
(home-page "https://github.com/timoast/signac/")
(synopsis "Analysis of single-cell chromatin data")
(description
@@ -15386,18 +15075,17 @@ sequence motif analysis.")
"1023hadgcsgi53kz53ql45207hfizf9sw57z0qij3ay1bx68zbpm"))))
(build-system python-build-system)
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-nose2" ,python-nose2)))
+ (list python-cython python-nose2))
;; The package mainly consists of a command-line tool, but also has a
;; Python-API. Thus these must be propagated.
(propagated-inputs
- `(("python-future" ,python-future)
- ("python-h5py" ,python-h5py)
- ("python-mappy" ,python-mappy)
- ("python-numpy" ,python-numpy)
- ("python-scipy" ,python-scipy)
- ("python-tqdm" ,python-tqdm)
- ("python-rpy2" ,python-rpy2)))
+ (list python-future
+ python-h5py
+ python-mappy
+ python-numpy
+ python-scipy
+ python-tqdm
+ python-rpy2))
(home-page "https://github.com/nanoporetech/tombo")
(synopsis "Analysis of raw nanopore sequencing data")
(description "Tombo is a suite of tools primarily for the identification of
@@ -15438,10 +15126,9 @@ for the analysis and visualization of raw nanopore signal.")
(delete-file-recursively (string-append
(site-packages inputs outputs)
"/vcf/test")))))))
- (native-inputs `(("python-cython" ,python-cython)))
+ (native-inputs (list python-cython))
(propagated-inputs
- `(("python-pysam" ,python-pysam)
- ("python-rpy2" ,python-rpy2)))
+ (list python-pysam python-rpy2))
(home-page "https://github.com/jamescasbon/PyVCF")
(synopsis "Variant Call Format parser for Python")
(description "This package provides a @acronym{VCF,Variant Call Format}
@@ -15460,9 +15147,7 @@ parser for Python.")
"1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg"))))
(build-system python-build-system)
(inputs
- `(("python-configparser" ,python-configparser)
- ("python-pysam" ,python-pysam)
- ("python-pyvcf" ,python-pyvcf)))
+ (list python-configparser python-pysam python-pyvcf))
(home-page "https://github.com/mroosmalen/nanosv")
(synopsis "Structural variation detection tool for Oxford Nanopore data.")
(description "NanoSV is a software package that can be used to identify
@@ -15484,10 +15169,9 @@ instruments, or Pacific Biosciences RSII or Sequel sequencers.")
"1z1gy8n56lhriy6hdkh9r82ndikndipq2cy2wh8q185qig4rimr6"))))
(build-system python-build-system)
(inputs
- `(("curl" ,curl)
- ("zlib" ,zlib)))
+ (list curl zlib))
(propagated-inputs
- `(("pybind11" ,pybind11)))
+ (list pybind11))
(home-page "https://github.com/aidenlab/straw")
(synopsis "Stream data from .hic files")
(description "Straw is library which allows rapid streaming of contact
@@ -15520,18 +15204,11 @@ data from @file{.hic} files. This package provides Python bindings.")
(with-directory-excursion "/tmp/tests"
(invoke "python" "-m" "pytest" "-v"))))))))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("python-pkgconfig" ,python-pkgconfig)
- ("python-pytest" ,python-pytest)))
+ (list pkg-config python-pkgconfig python-pytest))
(inputs
- `(("libpng" ,libpng)
- ("openssl" ,openssl)
- ("zlib" ,zlib)))
+ (list libpng openssl zlib))
(propagated-inputs
- `(("python-cython" ,python-cython)
- ("python-numpy" ,python-numpy)
- ("python-pandas" ,python-pandas)
- ("python-six" ,python-six)))
+ (list python-cython python-numpy python-pandas python-six))
(home-page "https://github.com/nvictus/pybbi")
(synopsis "Python bindings to UCSC Big Binary file library")
(description
@@ -15555,8 +15232,7 @@ feature is fast retrieval of range queries into numpy arrays.")
(build-system python-build-system)
(arguments '(#:tests? #false)) ; there are none
(propagated-inputs
- `(("python-biopython" ,python-biopython)
- ("python-matplotlib" ,python-matplotlib)))
+ (list python-biopython python-matplotlib))
(home-page
"https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer")
(synopsis "Plot features from DNA sequences")
@@ -15579,28 +15255,28 @@ e.g. from GenBank or Gff files, or Biopython SeqRecords.")
(build-system python-build-system)
(arguments '(#:tests? #false)) ; there are none
(inputs
- `(("pybind11" ,pybind11)))
+ (list pybind11))
(propagated-inputs
- `(("python-cooler" ,python-cooler)
- ("python-dna-features-viewer" ,python-dna-features-viewer)
- ("python-fire" ,python-fire)
- ("python-h5py" ,python-h5py)
- ("python-intervaltree" ,python-intervaltree)
- ("python-ipywidgets" ,python-ipywidgets)
- ("jupyter" ,jupyter)
- ("python-matplotlib" ,python-matplotlib)
- ("python-nbformat" ,python-nbformat)
- ("python-numpy" ,python-numpy)
- ("python-numpydoc" ,python-numpydoc)
- ("python-pandas" ,python-pandas)
- ("python-pybbi" ,python-pybbi)
- ("python-pytest" ,python-pytest)
- ("python-scipy" ,python-scipy)
- ("python-statsmodels" ,python-statsmodels)
- ("python-strawc" ,python-strawc)
- ("python-svgutils" ,python-svgutils)
- ("python-termcolor" ,python-termcolor)
- ("python-voila" ,python-voila)))
+ (list python-cooler
+ python-dna-features-viewer
+ python-fire
+ python-h5py
+ python-intervaltree
+ python-ipywidgets
+ jupyter
+ python-matplotlib
+ python-nbformat
+ python-numpy
+ python-numpydoc
+ python-pandas
+ python-pybbi
+ python-pytest
+ python-scipy
+ python-statsmodels
+ python-strawc
+ python-svgutils
+ python-termcolor
+ python-voila))
(home-page "https://github.com/GangCaoLab/CoolBox")
(synopsis "Genomic data visualization toolkit")
(description
@@ -15648,7 +15324,7 @@ browser.")
(add-installed-pythonpath inputs outputs)
(invoke "python" "tests/test_pyspoa.py")))))))
(propagated-inputs
- `(("pybind11" ,pybind11)))
+ (list pybind11))
(native-inputs
`(("cmake" ,cmake-minimal)))
(home-page "https://github.com/nanoporetech/pyspoa")
@@ -15685,11 +15361,9 @@ sequences")
;; problem with the C sources.
(delete 'sanity-check))))
(propagated-inputs
- `(("python-cffi" ,python-cffi)
- ("python-setuptools" ,python-setuptools)
- ("python-wheel" ,python-wheel)))
+ (list python-cffi python-setuptools python-wheel))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/ACEnglish/bwapy")
(synopsis "Python bindings to bwa alinger")
(description "This package provides Python bindings to the bwa mem
@@ -15722,21 +15396,21 @@ aligner.")
(substitute* "setup.py"
(("'sklearn',") "")))))))
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
(propagated-inputs
- `(("python-scikit-learn" ,python-scikit-learn)
- ("python-scipy" ,python-scipy)
- ("python-numpy" ,python-numpy)
- ("python-hmmlearn" ,python-hmmlearn)
- ("python-pandas" ,python-pandas)
- ("python-numba" ,python-numba)
- ("python-anndata" ,python-anndata)
- ("python-scanpy" ,python-scanpy)
- ("python-pybedtools" ,python-pybedtools)
- ("python-pysam" ,python-pysam)
- ("python-matplotlib" ,python-matplotlib)
- ("python-seaborn" ,python-seaborn)
- ("python-coolbox" ,python-coolbox)))
+ (list python-scikit-learn
+ python-scipy
+ python-numpy
+ python-hmmlearn
+ python-pandas
+ python-numba
+ python-anndata
+ python-scanpy
+ python-pybedtools
+ python-pysam
+ python-matplotlib
+ python-seaborn
+ python-coolbox))
(home-page "https://github.com/BIMSBbioinfo/scregseg")
(synopsis "Single-cell regulatory landscape segmentation")
(description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a
@@ -15795,15 +15469,9 @@ cross-cluster accessibility profiles.")
(copy-file "megadepth_dynamic"
(string-append bin "/megadepth"))))))))
(native-inputs
- `(("diffutils" ,diffutils)
- ("perl" ,perl)
- ("grep" ,grep)))
+ (list diffutils perl grep))
(inputs
- `(("curl" ,curl)
- ("htslib" ,htslib)
- ("libdeflate" ,libdeflate)
- ("libbigwig" ,libbigwig)
- ("zlib" ,zlib)))
+ (list curl htslib libdeflate libbigwig zlib))
(home-page "https://github.com/ChristopherWilks/megadepth")
(synopsis "BigWig and BAM/CRAM related utilities")
(description "Megadepth is an efficient tool for extracting coverage
@@ -15834,7 +15502,7 @@ both types of files.")
(lambda _
(chdir "ASCAT"))))))
(propagated-inputs
- `(("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-rcolorbrewer))
(home-page "https://github.com/VanLoo-lab/ascat/")
(synopsis "Allele-Specific Copy Number Analysis of Tumors in R")
(description "This package provides the @acronym{ASCAT,Allele-Specific Copy
@@ -15857,14 +15525,14 @@ ploidy and allele-specific copy number profiles.")
"0nmcq4c7y5g8h8lxsq9vadz9bj4qgqn118alip520ny6czaxki4h"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-devtools" ,r-devtools)
- ("r-readr" ,r-readr)
- ("r-doparallel" ,r-doparallel)
- ("r-ggplot2" ,r-ggplot2)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-gridextra" ,r-gridextra)
- ("r-gtools" ,r-gtools)
- ("r-ascat" ,r-ascat)))
+ (list r-devtools
+ r-readr
+ r-doparallel
+ r-ggplot2
+ r-rcolorbrewer
+ r-gridextra
+ r-gtools
+ r-ascat))
(home-page "https://github.com/Wedge-lab/battenberg")
(synopsis "Subclonal copy number estimation in R")
(description "This package contains the Battenberg R package for subclonal
@@ -15919,51 +15587,51 @@ value of physical insulation between neighboring domains.")
(properties `((upstream-name . "Spectre")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocmanager" ,r-biocmanager)
- ("r-caret" ,r-caret)
- ("r-class" ,r-class)
- ("r-colorramps" ,r-colorramps)
- ("r-data-table" ,r-data-table)
- ("r-devtools" ,r-devtools)
- ("r-dplyr" ,r-dplyr)
- ("r-exactextractr" ,r-exactextractr)
- ("r-factoextra" ,r-factoextra)
- ("r-flowcore" ,r-flowcore)
- ("r-flowsom" ,r-flowsom)
- ("r-flowviz" ,r-flowviz)
- ("r-fnn" ,r-fnn)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggpointdensity" ,r-ggpointdensity)
- ("r-ggpubr" ,r-ggpubr)
- ("r-ggraph" ,r-ggraph)
- ("r-ggthemes" ,r-ggthemes)
- ("r-gridextra" ,r-gridextra)
- ("r-gridextra" ,r-gridextra)
- ("r-gtools" ,r-gtools)
- ("r-hdf5array" ,r-hdf5array)
- ("r-irlba" ,r-irlba)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plyr" ,r-plyr)
- ("r-qs" ,r-qs)
- ("r-raster" ,r-raster)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rgeos" ,r-rgeos)
- ("r-rhdf5" ,r-rhdf5)
- ("r-rstudioapi" ,r-rstudioapi)
- ("r-rsvd" ,r-rsvd)
- ("r-rtsne" ,r-rtsne)
- ("r-s2" ,r-s2)
- ("r-scales" ,r-scales)
- ("r-sf" ,r-sf)
- ("r-sp" ,r-sp)
- ("r-stars" ,r-stars)
- ("r-stringr" ,r-stringr)
- ("r-tidygraph" ,r-tidygraph)
- ("r-tidyr" ,r-tidyr)
- ("r-tidyr" ,r-tidyr)
- ("r-tiff" ,r-tiff)
- ("r-umap" ,r-umap)))
+ (list r-biobase
+ r-biocmanager
+ r-caret
+ r-class
+ r-colorramps
+ r-data-table
+ r-devtools
+ r-dplyr
+ r-exactextractr
+ r-factoextra
+ r-flowcore
+ r-flowsom
+ r-flowviz
+ r-fnn
+ r-ggplot2
+ r-ggpointdensity
+ r-ggpubr
+ r-ggraph
+ r-ggthemes
+ r-gridextra
+ r-gridextra
+ r-gtools
+ r-hdf5array
+ r-irlba
+ r-pheatmap
+ r-plyr
+ r-qs
+ r-raster
+ r-rcolorbrewer
+ r-rgeos
+ r-rhdf5
+ r-rstudioapi
+ r-rsvd
+ r-rtsne
+ r-s2
+ r-scales
+ r-sf
+ r-sp
+ r-stars
+ r-stringr
+ r-tidygraph
+ r-tidyr
+ r-tidyr
+ r-tiff
+ r-umap))
(home-page "https://github.com/ImmuneDynamics/Spectre")
(synopsis "High-dimensional cytometry and imaging analysis")
(description
@@ -15991,16 +15659,16 @@ cytometry and imaging data.")
(properties `((upstream-name . "CytoNorm")))
(build-system r-build-system)
(propagated-inputs
- `(("r-cytoml" ,r-cytoml)
- ("r-dplyr" ,r-dplyr)
- ("r-emdist" ,r-emdist)
- ("r-flowcore" ,r-flowcore)
- ("r-flowsom" ,r-flowsom)
- ("r-flowworkspace" ,r-flowworkspace)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-pheatmap" ,r-pheatmap)
- ("r-stringr" ,r-stringr)))
+ (list r-cytoml
+ r-dplyr
+ r-emdist
+ r-flowcore
+ r-flowsom
+ r-flowworkspace
+ r-ggplot2
+ r-gridextra
+ r-pheatmap
+ r-stringr))
(home-page "https://github.com/saeyslab/CytoNorm")
(synopsis "Normalize cytometry data measured across multiple batches")
(description
@@ -16049,12 +15717,12 @@ interest.")
("guile" ,guile-3.0)
("guile-libyaml" ,guile-libyaml)))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("lzip" ,lzip)
- ;; To build documentation
- ("cwltool" ,cwltool)
- ("graphviz" ,graphviz)
- ("skribilo" ,skribilo)))
+ (list pkg-config
+ lzip
+ ;; To build documentation
+ cwltool
+ graphviz
+ skribilo))
(home-page "https://ccwl.systemreboot.net")
(synopsis "Concise common workflow language")
(description "The @acronym{ccwl, Concise Common Workflow Language} is a