diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 170 |
1 files changed, 124 insertions, 46 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8514306f94..39611d23f4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> @@ -2822,6 +2822,86 @@ sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.") (license license:gpl3+))) +(define-public trf + (package + (name "trf") + (version "4.09.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Benson-Genomics-Lab/TRF") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0fhwr4s1mf8nw8fr5imwjvjr42b59p97zr961ifm8xl1bajz4wpg")))) + (build-system gnu-build-system) + (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 +copies of a pattern of nucleotides. Tandem Repeats Finder is a program to +locate and display tandem repeats in DNA sequences. In order to use the +program, the user submits a sequence in FASTA format. The output consists of +two files: a repeat table file and an alignment file. Submitted sequences may +be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 +bases are detected.") + (license license:agpl3+))) + +(define-public repeat-masker + (package + (name "repeat-masker") + (version "4.1.1") + (source (origin + (method url-fetch) + (uri (string-append "http://www.repeatmasker.org/" + "RepeatMasker/RepeatMasker-" + version ".tar.gz")) + (sha256 + (base32 "03144sl9kh5ni2i33phi7x2pjndzbm5bjw3r4kqvmm6hxyb4k4x2")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #false ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((share (string-append (assoc-ref outputs "out") + "/share/RepeatMasker"))) + (mkdir-p share) + (copy-recursively "." share) + (with-directory-excursion share + (invoke "perl" "configure" + "--trf_prgm" (which "trf") + "--hmmer_dir" + (string-append (assoc-ref inputs "hmmer") + "/bin")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/RepeatMasker")) + (bin (string-append out "/bin")) + (path (getenv "PERL5LIB"))) + (install-file (string-append share "/RepeatMasker") bin) + (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))) + (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 +copies of a pattern of nucleotides. Tandem Repeats Finder is a program to +locate and display tandem repeats in DNA sequences. In order to use the +program, the user submits a sequence in FASTA format. The output consists of +two files: a repeat table file and an alignment file. Submitted sequences may +be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 +bases are detected.") + (license license:osl2.1))) + (define-public diamond (package (name "diamond") @@ -7189,6 +7269,45 @@ between two different types of motif instances using as much relevant information as possible.") (license (list license:gpl2+ license:gpl3+)))) +(define-public r-demultiplex + (let ((commit "6e2a1422c8e6f418cfb271997eebc91f9195f299") + (revision "1")) + (package + (name "r-demultiplex") + (version (git-version "1.0.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chris-mcginnis-ucsf/MULTI-seq") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01kv88wp8vdaq07sjk0d3d1cb553mq1xqg0war81pgmg63bgi38w")))) + (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))) + (home-page "https://github.com/chris-mcginnis-ucsf/MULTI-seq") + (synopsis "MULTI-seq pre-processing and classification tools") + (description + "deMULTIplex is an R package for analyzing single-cell RNA sequencing +data generated with the MULTI-seq sample multiplexing method. The package +includes software to + +@enumerate +@item Convert raw MULTI-seq sample barcode library FASTQs into a sample + barcode UMI count matrix, and +@item Classify cell barcodes into sample barcode groups. +@end enumerate +") + (license license:cc0)))) + (define-public r-genefilter (package (name "r-genefilter") @@ -15090,18 +15209,18 @@ library automatically handles index file generation and use.") (let* ((out (assoc-ref outputs "out")) (pkgconfig (string-append out "/lib/pkgconfig"))) (mkdir-p pkgconfig) - (with-output-to-file (string-append pkgconfig "/libvcflib.pc") + (with-output-to-file (string-append pkgconfig "/vcflib.pc") (lambda _ (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ ~@ - Name: libvcflib~@ + Name: vcflib~@ Version: ~a~@ - Requires: smithwaterman, fastahack~@ + Requires: smithwaterman, fastahack, tabixpp~@ Description: C++ library for parsing and manipulating VCF files~@ - Libs: -L${libdir} -llibvcflib~@ + Libs: -L${libdir} -lvcflib~@ Cflags: -I${includedir}~%" out ,version))) #t)))))) @@ -15488,44 +15607,3 @@ biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.") (license license:lgpl2.1+))) - -(define-public grocsvs - ;; The last release is out of date and new features have been added. - (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d") - (revision "1")) - (package - (name "grocsvs") - (version (git-version "0.2.6.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/grocsvs/grocsvs") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc")) - (patches (search-patches "grocsvs-dont-use-admiral.patch")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; No test suite. - #:python ,python-2)) ; Only python-2 supported. - (inputs - `(("python2-h5py" ,python2-h5py) - ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper) - ("python2-networkx" ,python2-networkx) - ("python2-psutil" ,python2-psutil) - ("python2-pandas" ,python2-pandas) - ("python2-pybedtools" ,python2-pybedtools) - ("python2-pyfaidx" ,python2-pyfaidx) - ("python2-pygraphviz" ,python2-pygraphviz) - ("python2-pysam" ,python2-pysam) - ("python2-scipy" ,python2-scipy))) - (home-page "https://github.com/grocsvs/grocsvs") - (synopsis "Genome-wide reconstruction of complex structural variants") - (description - "@dfn{Genome-wide Reconstruction of Complex Structural Variants} -(GROC-SVs) is a software pipeline for identifying large-scale structural -variants, performing sequence assembly at the breakpoints, and reconstructing -the complex structural variants using the long-fragment information from the -10x Genomics platform.") - (license license:expat)))) |