diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 400 |
1 files changed, 286 insertions, 114 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 773b5909b6..415024fadc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -50,6 +50,7 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages datastructures) #:use-module (gnu packages file) + #:use-module (gnu packages flex) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages gd) @@ -215,8 +216,7 @@ structure of the predicted RNA.") ("libtool" ,libtool) ("zlib" ,zlib) ("python-nose" ,python2-nose) - ("python-pysam" ,python2-pysam) - ("python-setuptools" ,python2-setuptools))) + ("python-pysam" ,python2-pysam))) (inputs `(("htslib" ,htslib) ("samtools" ,samtools) @@ -523,15 +523,14 @@ intended to behave exactly the same as the original BWK awk.") (build-system python-build-system) (arguments `(#:python ,python-2)) ; no Python 3 support (inputs - `(("python-cython" ,python2-cython) - ("python-matplotlib" ,python2-matplotlib))) + `(("python-matplotlib" ,python2-matplotlib))) (propagated-inputs `(("bedtools" ,bedtools) ("samtools" ,samtools))) (native-inputs - `(("python-pyyaml" ,python2-pyyaml) - ("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + `(("python-cython" ,python2-cython) + ("python-pyyaml" ,python2-pyyaml) + ("python-nose" ,python2-nose))) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -586,9 +585,7 @@ e.g. microbiome samples, genomes, metagenomes.") (substitute* "setup.py" (("install_requires.append\\(\"pyqi\"\\)") "pass")) #t))) - ,@(package-arguments base))) - (native-inputs `(("python2-setuptools" ,python2-setuptools) - ,@(package-native-inputs base)))))) + ,@(package-arguments base)))))) (define-public bioperl-minimal (let* ((inputs `(("perl-module-build" ,perl-module-build) @@ -673,7 +670,7 @@ provide a coordinated and extensible framework to do computational biology.") (add-before 'check 'set-home ;; Some tests require a home directory to be set. (lambda _ (setenv "HOME" "/tmp") #t))))) - (inputs + (propagated-inputs `(("python-numpy" ,python-numpy))) (home-page "http://biopython.org/") (synopsis "Tools for biological computation in Python") @@ -684,15 +681,10 @@ bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.") - (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")) - (properties `((python2-variant . ,(delay python2-biopython)))))) + (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) (define-public python2-biopython - (let ((base (package-with-python2 (strip-python2-variant python-biopython)))) - (package - (inherit base) - (native-inputs `(("python2-setuptools" ,python2-setuptools) - ,@(package-native-inputs base)))))) + (package-with-python2 python-biopython)) ;; An outdated version of biopython is required for seqmagick, see ;; https://github.com/fhcrc/seqmagick/issues/59 @@ -1339,8 +1331,7 @@ well as many of the command line options.") `(("python-numpy" ,python2-numpy) ("zlib" ,zlib))) (native-inputs - `(("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + `(("python-nose" ,python2-nose))) (home-page "http://bitbucket.org/james_taylor/bx-python/") (synopsis "Tools for manipulating biological data") (description @@ -1404,7 +1395,6 @@ multiple sequence alignments.") ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python-cython) - ("python-setuptools" ,python-setuptools) ;; Dependencies below are are for tests only. ("samtools" ,samtools) ("bcftools" ,bcftools) @@ -1430,7 +1420,6 @@ also includes an interface for tabix.") (sha256 (base32 "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) - (properties `((python2-variant . ,(delay python2-twobitreader)))) (build-system python-build-system) (arguments '(;; Tests are not distributed in the PyPi release. @@ -1447,11 +1436,7 @@ UCSC genome browser.") (license license:artistic2.0))) (define-public python2-twobitreader - (let ((base (package-with-python2 (strip-python2-variant python-twobitreader)))) - (package - (inherit base) - (native-inputs `(("python2-setuptools" ,python2-setuptools) - ,@(package-native-inputs base)))))) + (package-with-python2 python-twobitreader)) (define-public python-plastid (package @@ -1463,7 +1448,6 @@ UCSC genome browser.") (sha256 (base32 "1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj")))) - (properties `((python2-variant . ,(delay python2-plastid)))) (build-system python-build-system) (arguments ;; Some test files are not included. @@ -1488,12 +1472,7 @@ high-throughput sequencing data – with an emphasis on simplicity.") (license license:bsd-3))) (define-public python2-plastid - (let ((base (package-with-python2 (strip-python2-variant python-plastid)))) - (package - (inherit base) - ;; setuptools is required at runtime - (propagated-inputs `(("python2-setuptools" ,python2-setuptools) - ,@(package-propagated-inputs base)))))) + (package-with-python2 python-plastid)) (define-public cd-hit (package @@ -1580,9 +1559,8 @@ databases.") ("python-numpy" ,python2-numpy) ("python-scipy" ,python2-scipy))) (native-inputs - `(("python-mock" ,python2-mock) ; for tests - ("python-pytz" ,python2-pytz) ; for tests - ("python-setuptools" ,python2-setuptools))) + `(("python-mock" ,python2-mock) ; for tests + ("python-pytz" ,python2-pytz))) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") (description @@ -1755,8 +1733,7 @@ time.") ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python2-cython) - ("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + ("python-nose" ,python2-nose))) (home-page "http://crossmap.sourceforge.net/") (synopsis "Convert genome coordinates between assemblies") (description @@ -1854,8 +1831,7 @@ preparation protocols.") (alist-delete 'check %standard-phases)))) (native-inputs `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("python-setuptools" ,python-setuptools))) + ("python-nose" ,python-nose))) (home-page "https://code.google.com/p/cutadapt/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description @@ -1945,10 +1921,7 @@ accessing bigWig files.") (license license:expat))) (define-public python2-pybigwig - (let ((pybigwig (package-with-python2 python-pybigwig))) - (package (inherit pybigwig) - (native-inputs - `(("python-setuptools" ,python2-setuptools)))))) + (package-with-python2 python-pybigwig)) (define-public python-dendropy (package @@ -1997,8 +1970,7 @@ trees (phylogenies) and characters.") ;; There is currently a test failure that only happens on some ;; systems, and only using "setup.py test" (lambda _ (zero? (system* "nosetests"))))))) - (native-inputs `(("python2-setuptools" ,python2-setuptools) - ("python2-nose" ,python2-nose) + (native-inputs `(("python2-nose" ,python2-nose) ,@(package-native-inputs base)))))) @@ -2026,9 +1998,8 @@ trees (phylogenies) and characters.") ("python-pysam" ,python2-pysam) ("python-pybigwig" ,python2-pybigwig))) (native-inputs - `(("python-mock" ,python2-mock) ;for tests - ("python-pytz" ,python2-pytz) ;for tests - ("python-setuptools" ,python2-setuptools))) + `(("python-mock" ,python2-mock) ;for tests + ("python-pytz" ,python2-pytz))) ;for tests (home-page "https://github.com/fidelram/deepTools") (synopsis "Tools for normalizing and visualizing deep-sequencing data") (description @@ -2683,8 +2654,7 @@ comment or quality sections.") ("python-pysam" ,python2-pysam) ("python-networkx" ,python2-networkx))) (native-inputs - `(("python-cython" ,python2-cython) - ("python-setuptools" ,python2-setuptools))) + `(("python-cython" ,python2-cython))) (home-page "http://grit-bio.org") (synopsis "Tool for integrative analysis of RNA-seq type assays") (description @@ -2810,8 +2780,6 @@ HMMs).") `(("python-numpy" ,python2-numpy))) (inputs `(("python-pysam" ,python2-pysam))) - (native-inputs - `(("python-setuptools" ,python2-setuptools))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -2932,8 +2900,7 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") ("python-numpy" ,python-numpy) ("python-matplotlib" ,python-matplotlib))) (native-inputs - `(("python-cython" ,python-cython) - ("python-setuptools" ,python-setuptools))) + `(("python-cython" ,python-cython))) (home-page "https://github.com/nboley/idr") (synopsis "Tool to measure the irreproducible discovery rate (IDR)") (description @@ -3090,8 +3057,6 @@ data.") #:tests? #f)) ; no test target (inputs `(("python-numpy" ,python2-numpy))) - (native-inputs - `(("python-setuptools" ,python2-setuptools))) (home-page "http://github.com/taoliu/MACS/") (synopsis "Model based analysis for ChIP-Seq data") (description @@ -3423,9 +3388,8 @@ linker_so='gcc -shared'); defines"))))) ("python-scipy" ,python2-scipy) ("python-matplotlib" ,python2-matplotlib))) (native-inputs - `(("python-mock" ,python2-mock) ;for tests - ("python-pytz" ,python2-pytz) ;for tests - ("python-setuptools" ,python2-setuptools))) + `(("python-mock" ,python2-mock) ;for tests + ("python-pytz" ,python2-pytz))) ;for tests (home-page "http://genes.mit.edu/burgelab/miso/index.html") (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") (description @@ -3472,6 +3436,45 @@ program for nucleotide and protein sequences.") ;; License information found in 'muscle -h' and usage.cpp. (license license:public-domain))) +(define-public newick-utils + ;; There are no recent releases so we package from git. + (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87")) + (package + (name "newick-utils") + (version (string-append "1.6-1." (string-take commit 8))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tjunier/newick_utils.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autoconf + (lambda _ (zero? (system* "autoreconf" "-vif"))))))) + (inputs + ;; XXX: TODO: Enable Lua and Guile bindings. + ;; https://github.com/tjunier/newick_utils/issues/13 + `(("libxml2" ,libxml2) + ("flex" ,flex) + ("bison" ,bison))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (synopsis "Programs for working with newick format phylogenetic trees") + (description + "Newick-utils is a suite of utilities for processing phylogenetic trees +in Newick format. Functions include re-rooting, extracting subtrees, +trimming, pruning, condensing, drawing (ASCII graphics or SVG).") + (home-page "https://github.com/tjunier/newick_utils") + (license license:bsd-3)))) + (define-public orfm (package (name "orfm") @@ -3509,18 +3512,15 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) (build-system python-build-system) (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 - (inputs + (propagated-inputs `(("python-cython" ,python2-cython) ("python-numpy" ,python2-numpy) ("python-pysam" ,python2-pysam) ("python-h5py" ,python2-h5py))) (native-inputs - `(("python-docutils" ,python2-docutils) - ("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools) - ("python-sphinx" ,python2-sphinx))) - (propagated-inputs - `(("python-pyxb" ,python2-pyxb))) + `(("python-nose" ,python2-nose) + ("python-sphinx" ,python2-sphinx) + ("python-pyxb" ,python2-pyxb))) (home-page "http://pacificbiosciences.github.io/pbcore/") (synopsis "Library for reading and writing PacBio data files") (description @@ -3543,18 +3543,7 @@ files and writing bioinformatics applications.") "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; requires Python 2.7 - #:phases - (modify-phases %standard-phases - (add-after - 'install 'remove-bin-directory - (lambda* (#:key outputs #:allow-other-keys) - ;; The "bin" directory only contains wrappers for running - ;; the module tests. They are not needed after the - ;; "check" phase. - (delete-file-recursively - (string-append (assoc-ref outputs "out") "/bin")) - #t))))) + `(#:python ,python-2)) ; requires Python 2.7 (propagated-inputs `(("python-scipy" ,python2-scipy) ("python-numpy" ,python2-numpy) @@ -3563,8 +3552,7 @@ files and writing bioinformatics applications.") ("python-pandas" ,python2-pandas) ("python-pysnptools" ,python2-pysnptools))) (native-inputs - `(("python-setuptools" ,python2-setuptools) - ("python-mock" ,python2-mock) + `(("python-mock" ,python2-mock) ("python-nose" ,python2-nose) ("unzip" ,unzip))) (home-page "https://github.com/PMBio/warpedLMM") @@ -3598,11 +3586,6 @@ the phenotype as it models the data.") (build-system python-build-system) (arguments `(#:python ,python-2 - ;; With standard flags, the install phase attempts to create a zip'd - ;; egg file, and fails with an error: 'ZIP does not support timestamps - ;; before 1980' - #:configure-flags '("--single-version-externally-managed" - "--record=pbtranscript-tofu.txt") #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-directory @@ -3626,8 +3609,7 @@ the phenotype as it models the data.") ("python-h5py" ,python2-h5py))) (native-inputs `(("python-cython" ,python2-cython) - ("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + ("python-nose" ,python2-nose))) (home-page "https://github.com/PacificBiosciences/cDNA_primer") (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") (description @@ -3693,6 +3675,58 @@ for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.") (license license:gpl2+))) +(define-public proteinortho + (package + (name "proteinortho") + (version "5.15") + (source + (origin + (method url-fetch) + (uri + (string-append + "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" + version "_src.tar.gz")) + (sha256 + (base32 + "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (replace 'configure + ;; There is no configure script, so we modify the Makefile directly. + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("INSTALLDIR=.*") + (string-append + "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))) + #t)) + (add-before 'install 'make-install-directory + ;; The install directory is not created during 'make install'. + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) + #t)) + (add-after 'install 'wrap-programs + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((path (getenv "PATH")) + (out (assoc-ref outputs "out")) + (binary (string-append out "/bin/proteinortho5.pl"))) + (wrap-program binary `("PATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("perl" ,perl) + ("python" ,python-2) + ("blast+" ,blast+))) + (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") + (synopsis "Detect orthologous genes across species") + (description + "Proteinortho is a tool to detect orthologous genes across different +species. For doing so, it compares similarities of given gene sequences and +clusters them to find significant groups. The algorithm was designed to handle +large-scale data and can be applied to hundreds of species at once.") + (license license:gpl2+))) + (define-public pyicoteo (package (name "pyicoteo") @@ -3765,7 +3799,7 @@ partial genes, and identifies translation initiation sites.") (define-public roary (package (name "roary") - (version "3.6.8") + (version "3.7.0") (source (origin (method url-fetch) @@ -3774,7 +3808,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw")))) + "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43")))) (build-system perl-build-system) (arguments `(#:phases @@ -4024,7 +4058,6 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") `(("python-cython" ,python2-cython) ("python-pysam" ,python2-pysam) ("python-numpy" ,python2-numpy) - ("python-setuptools" ,python2-setuptools) ("zlib" ,zlib))) (native-inputs `(("python-nose" ,python2-nose))) @@ -4586,11 +4619,7 @@ sequence itself can be retrieved from these databases.") (license license:bsd-3))) (define-public python2-screed - (let ((base (package-with-python2 (strip-python2-variant python-screed)))) - (package - (inherit base) - (native-inputs `(("python2-setuptools" ,python2-setuptools) - ,@(package-native-inputs base)))))) + (package-with-python2 python-screed)) (define-public sra-tools (package @@ -4752,8 +4781,7 @@ bioinformatics file formats, sequence alignment, and more.") ;; should be removed. `(("python-biopython" ,python2-biopython-1.66))) (native-inputs - `(("python-setuptools" ,python2-setuptools) - ("python-nose" ,python2-nose))) + `(("python-nose" ,python2-nose))) (home-page "http://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description @@ -7246,6 +7274,29 @@ two-dimensional genome scans.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public r-r4rna + (package + (name "r-r4rna") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_" + version ".tar.gz")) + (sha256 + (base32 + "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) + (build-system r-build-system) + (propagated-inputs + `(("r-optparse" ,r-optparse) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "http://www.e-rna.org/r-chie/index.cgi") + (synopsis "Analysis framework for RNA secondary structure") + (description + "The R4RNA package aims to be a general framework for the analysis of RNA +secondary structure and comparative analysis in R.") + (license license:gpl3+))) + (define-public r-rhtslib (package (name "r-rhtslib") @@ -7426,6 +7477,141 @@ characterization and visualization of a wide range of mutational patterns in SNV base substitution data.") (license license:expat))) +(define-public r-wgcna + (package + (name "r-wgcna") + (version "1.51") + (source + (origin + (method url-fetch) + (uri (cran-uri "WGCNA" version)) + (sha256 + (base32 + "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx")))) + (properties `((upstream-name . "WGCNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-doparallel" ,r-doparallel) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-fastcluster" ,r-fastcluster) + ("r-foreach" ,r-foreach) + ("r-go-db" ,r-go-db) + ("r-hmisc" ,r-hmisc) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-preprocesscore" ,r-preprocesscore))) + (home-page + "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") + (synopsis "Weighted correlation network analysis") + (description + "This package provides functions necessary to perform Weighted +Correlation Network Analysis on high-dimensional data. It includes functions +for rudimentary data cleaning, construction and summarization of correlation +networks, module identification and functions for relating both variables and +modules to sample traits. It also includes a number of utility functions for +data manipulation and visualization.") + (license license:gpl2+))) + +(define-public r-chipkernels + (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") + (revision "1")) + (package + (name "r-chipkernels") + (version (string-append "1.1-" revision "." (string-take commit 9))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ManuSetty/ChIPKernels.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "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))) + (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 +kernels used for DNA Sequence analysis. A dictionary of the desired kernel +must be built and this dictionary can be used for determining kernels for DNA +Sequences.") + (license license:gpl2+)))) + +(define-public r-seqgl + (package + (name "r-seqgl") + (version "1.1.4") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ManuSetty/SeqGL/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) + (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))) + (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 +transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. +This package presents a method which uses group lasso to discriminate between +bound and non bound genomic regions to accurately identify transcription +factors bound at the specific regions.") + (license license:gpl2+))) + +(define-public r-gkmsvm + (package + (name "r-gkmsvm") + (version "0.71.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gkmSVM" version)) + (sha256 + (base32 + "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0")))) + (properties `((upstream-name . "gkmSVM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-kernlab" ,r-kernlab) + ("r-rcpp" ,r-rcpp) + ("r-rocr" ,r-rocr) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr))) + (home-page "http://cran.r-project.org/web/packages/gkmSVM") + (synopsis "Gapped-kmer support vector machine") + (description + "This R package provides tools for training gapped-kmer SVM classifiers +for DNA and protein sequences. This package supports several sequence +kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") + (license license:gpl2+))) + (define-public emboss (package (name "emboss") @@ -7615,19 +7801,7 @@ may optionally be provided to further inform the peak-calling process.") (build-system python-build-system) (arguments `(#:python ,python-2 ; python2 only - #:tests? #f ; no tests included - #:phases - (modify-phases %standard-phases - ;; When setuptools is used a ".egg" archive is generated and - ;; installed. This makes it hard to actually run PePr. This issue - ;; has been reported upstream: - ;; https://github.com/shawnzhangyx/PePr/issues/9 - (add-after 'unpack 'disable-egg-generation - (lambda _ - (substitute* "setup.py" - (("from setuptools import setup") - "from distutils.core import setup")) - #t))))) + #:tests? #f)) ; no tests included (propagated-inputs `(("python2-numpy" ,python2-numpy) ("python2-scipy" ,python2-scipy) @@ -7689,8 +7863,6 @@ replacement for strverscmp.") ("python-click" ,python-click) ("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy))) - (native-inputs - `(("python-setuptools" ,python-setuptools))) (home-page "http://multiqc.info") (synopsis "Aggregate bioinformatics analysis reports") (description |