;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages graph)
#:use-module (gnu packages groff)
#:use-module (gnu packages guile)
+ #:use-module (gnu packages guile-xyz)
#:use-module (gnu packages haskell)
#:use-module (gnu packages haskell-check)
#:use-module (gnu packages haskell-web)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages dlang)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages lisp)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages man)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-compression)
#:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
(define-public python-pybedtools
(package
(name "python-pybedtools")
- (version "0.7.10")
+ (version "0.8.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
- "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji"))))
+ "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:modules ((ice-9 ftw)
+ (srfi srfi-1)
+ (srfi srfi-26)
+ (guix build utils)
+ (guix build python-build-system))
+ ;; See https://github.com/daler/pybedtools/issues/192
+ #:phases
(modify-phases %standard-phases
;; See https://github.com/daler/pybedtools/issues/261
(add-after 'unpack 'disable-broken-tests
(substitute* "pybedtools/test/test_scripts.py"
(("def test_venn_mpl")
"def _do_not_test_venn_mpl"))
- ;; Requires internet access.
(substitute* "pybedtools/test/test_helpers.py"
+ ;; Requires internet access.
(("def test_chromsizes")
- "def _do_not_test_chromsizes"))
- ;; FIXME: these two fail for no good reason.
- (substitute* "pybedtools/test/test1.py"
- (("def test_issue_157")
- "def _do_not_test_issue_157")
- (("def test_to_dataframe")
- "def _do_not_test_to_dataframe"))
- #t)))))
- (propagated-inputs
- ;; Tests don't pass with Bedtools 2.27.1.
- ;; See https://github.com/daler/pybedtools/issues/260
- `(("bedtools" ,bedtools-2.26)
+ "def _do_not_test_chromsizes")
+ ;; Broken as a result of the workaround used in the check phase
+ ;; (see: https://github.com/daler/pybedtools/issues/192).
+ (("def test_getting_example_beds")
+ "def _do_not_test_getting_example_beds"))
+ #t))
+ ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
+ ;; build system.
+ ;; Force the Cythonization of C++ files to guard against compilation
+ ;; problems.
+ (add-after 'unpack 'remove-cython-generated-files
+ (lambda _
+ (let ((cython-sources (map (cut string-drop-right <> 4)
+ (find-files "." "\\.pyx$")))
+ (c/c++-files (find-files "." "\\.(c|cpp|cxx)$")))
+ (define (strip-extension filename)
+ (string-take filename (string-index-right filename #\.)))
+ (define (cythonized? c/c++-file)
+ (member (strip-extension c/c++-file) cython-sources))
+ (for-each delete-file (filter cythonized? c/c++-files))
+ #t)))
+ (add-after 'remove-cython-generated-files 'generate-cython-extensions
+ (lambda _
+ (invoke "python" "setup.py" "cythonize")))
+ (replace 'check
+ (lambda _
+ (let* ((cwd (getcwd))
+ (build-root-directory (string-append cwd "/build/"))
+ (build (string-append
+ build-root-directory
+ (find (cut string-prefix? "lib" <>)
+ (scandir (string-append
+ build-root-directory)))))
+ (scripts (string-append
+ build-root-directory
+ (find (cut string-prefix? "scripts" <>)
+ (scandir build-root-directory)))))
+ (setenv "PYTHONPATH"
+ (string-append build ":" (getenv "PYTHONPATH")))
+ ;; Executable scripts such as 'intron_exon_reads.py' must be
+ ;; available in the PATH.
+ (setenv "PATH"
+ (string-append scripts ":" (getenv "PATH"))))
+ ;; The tests need to be run from elsewhere...
+ (mkdir-p "/tmp/test")
+ (copy-recursively "pybedtools/test" "/tmp/test")
+ (with-directory-excursion "/tmp/test"
+ (invoke "pytest")))))))
+ (propagated-inputs
+ `(("bedtools" ,bedtools)
("samtools" ,samtools)
("python-matplotlib" ,python-matplotlib)
("python-pysam" ,python-pysam)
`(("python-numpy" ,python-numpy)
("python-pandas" ,python-pandas)
("python-cython" ,python-cython)
- ("python-nose" ,python-nose)
- ("kentutils" ,kentutils) ; for bedGraphToBigWig
- ("python-six" ,python-six)))
+ ("kentutils" ,kentutils) ; for bedGraphToBigWig
+ ("python-six" ,python-six)
+ ;; For the test suite.
+ ("python-pytest" ,python-pytest)
+ ("python-psutil" ,python-psutil)))
(home-page "https://pythonhosted.org/pybedtools/")
(synopsis "Python wrapper for BEDtools programs")
(description
(license license:gpl2+)))
(define-public python2-pybedtools
- (let ((pkg (package-with-python2 python-pybedtools)))
- (package (inherit pkg)
- (arguments
- `(#:modules ((ice-9 ftw)
- (srfi srfi-1)
- (srfi srfi-26)
- (guix build utils)
- (guix build python-build-system))
- ;; See https://github.com/daler/pybedtools/issues/192
- ,@(substitute-keyword-arguments (package-arguments pkg)
- ((#:phases phases)
- `(modify-phases ,phases
- (replace 'check
- (lambda _
- (let ((cwd (getcwd)))
- (setenv "PYTHONPATH"
- (string-append cwd "/build/"
- (find (cut string-prefix? "lib" <>)
- (scandir (string-append cwd "/build")))
- ":" (getenv "PYTHONPATH"))))
- ;; The tests need to be run from elsewhere...
- (mkdir-p "/tmp/test")
- (copy-recursively "pybedtools/test" "/tmp/test")
- (with-directory-excursion "/tmp/test"
- (invoke "nosetests"
- ;; This test fails for unknown reasons
- "--exclude=.*test_getting_example_beds"))
- #t))))))))))
+ (package-with-python2 python-pybedtools))
(define-public python-biom-format
(package
(supported-systems '("x86_64-linux"))
(license license:gpl3+)))
+(define-public bowtie1
+ (package
+ (name "bowtie1")
+ (version "1.2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/"
+ version "/bowtie-" version "-src.zip"))
+ (sha256
+ (base32
+ "1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* "Makefile"
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+ (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ; no "check" target
+ #:make-flags
+ (list "all"
+ (string-append "prefix=" (assoc-ref %outputs "out")))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure))))
+ (inputs
+ `(("tbb" ,tbb)
+ ("zlib" ,zlib)))
+ (supported-systems '("x86_64-linux"))
+ (home-page "http://bowtie-bio.sourceforge.net/index.shtml")
+ (synopsis "Fast aligner for short nucleotide sequence reads")
+ (description
+ "Bowtie is a fast, memory-efficient short read aligner. It aligns short
+DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
+reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to
+keep its memory footprint small: typically about 2.2 GB for the human
+genome (2.9 GB for paired-end).")
+ (license license:artistic2.0)))
+
(define-public tophat
(package
(name "tophat")
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'fix-latex-errors
+ (lambda _
+ (with-fluids ((%default-port-encoding #f))
+ (substitute* "doc/references.bib"
+ (("\\{S\\}illanp[^,]+,")
+ "{S}illanp{\\\"a}{\\\"a},")))
+ ;; XXX: I just can't get pdflatex to not complain about these
+ ;; characters. They end up in the manual via the generated
+ ;; discrover-cli-help.txt.
+ (substitute* "src/hmm/cli.cpp"
+ (("µ") "mu")
+ (("η") "eta")
+ (("≤") "<="))
+ ;; This seems to be a syntax error.
+ (substitute* "doc/discrover-manual.tex"
+ (("theverbbox\\[t\\]") "theverbbox"))
+ #t))
(add-after 'unpack 'add-missing-includes
(lambda _
(substitute* "src/executioninformation.hpp"
(substitute* "src/plasma/fasta.hpp"
(("#define FASTA_HPP" line)
(string-append line "\n#include <random>")))
- #t)))))
+ #t))
+ ;; FIXME: this is needed because we're using texlive-union, which
+ ;; doesn't handle fonts correctly. It expects to be able to generate
+ ;; fonts in the home directory.
+ (add-before 'build 'setenv-HOME
+ (lambda _ (setenv "HOME" "/tmp") #t)))))
(inputs
`(("boost" ,boost)
- ("cairo" ,cairo)))
+ ("cairo" ,cairo)
+ ("rmath-standalone" ,rmath-standalone)))
(native-inputs
- `(("texlive" ,texlive)
- ;; TODO: Replace texlive with minimal texlive-union.
- ;; ("texlive" ,(texlive-union (list texlive-latex-doi
- ;; texlive-latex-hyperref
- ;; texlive-latex-oberdiek
- ;; texlive-generic-ifxetex
- ;; texlive-latex-url
- ;; texlive-latex-pgf
- ;; texlive-latex-examplep
- ;; texlive-latex-natbib
- ;; texlive-latex-verbatimbox
- ;; texlive-latex-ms
- ;; texlive-latex-xcolor
- ;; texlive-fonts-amsfonts
- ;; texlive-latex-amsfonts
- ;; ;; ...
- ;; )))
+ `(("texlive" ,(texlive-union (list texlive-fonts-cm
+ texlive-fonts-amsfonts
+
+ texlive-latex-doi
+ texlive-latex-examplep
+ texlive-latex-hyperref
+ texlive-latex-ms
+ texlive-latex-natbib
+ texlive-bibtex ; style files used by natbib
+ texlive-latex-pgf ; tikz
+ texlive-latex-verbatimbox)))
("imagemagick" ,imagemagick)))
(home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
(synopsis "Discover discriminative nucleotide sequence motifs")
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'do-not-tune-to-CPU
+ (lambda _
+ (substitute* "src/CMakeLists.txt"
+ ((" -march=native") ""))
+ #t))
(replace 'check
(lambda* (#:key outputs #:allow-other-keys)
(setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
(home-page "https://github.com/wwood/OrfM")
(license license:lgpl3+)))
-(define-public pplacer
- (let ((commit "807f6f3"))
- (package
- (name "pplacer")
- ;; The commit should be updated with each version change.
- (version "1.1.alpha19")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/matsen/pplacer.git")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
- (build-system ocaml-build-system)
- (arguments
- `(#:ocaml ,ocaml-4.01
- #:findlib ,ocaml4.01-findlib
- #:modules ((guix build ocaml-build-system)
- (guix build utils)
- (ice-9 ftw))
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (add-after 'unpack 'replace-bundled-cddlib
- (lambda* (#:key inputs #:allow-other-keys)
- (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
- (local-dir "cddlib_guix"))
- (mkdir local-dir)
- (with-directory-excursion local-dir
- (invoke "tar" "xvf" cddlib-src))
- (let ((cddlib-src-folder
- (string-append local-dir "/"
- (list-ref (scandir local-dir) 2)
- "/lib-src")))
- (for-each make-file-writable (find-files "cdd_src" ".*"))
- (for-each
- (lambda (file)
- (copy-file file
- (string-append "cdd_src/" (basename file))))
- (find-files cddlib-src-folder ".*[ch]$")))
- #t)))
- (add-after 'unpack 'fix-makefile
- (lambda _
- ;; Remove system calls to 'git'.
- (substitute* "Makefile"
- (("^DESCRIPT:=pplacer-.*")
- (string-append
- "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
- (substitute* "myocamlbuild.ml"
- (("git describe --tags --long .*\\\" with")
- (string-append
- "echo -n v" ,version "-" ,commit "\" with")))
- #t))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (copy-recursively "bin" bin))
- #t)))))
- (native-inputs
- `(("zlib" ,zlib)
- ("gsl" ,gsl)
- ("ocaml-ounit" ,ocaml4.01-ounit)
- ("ocaml-batteries" ,ocaml4.01-batteries)
- ("ocaml-camlzip" ,ocaml4.01-camlzip)
- ("ocaml-csv" ,ocaml4.01-csv)
- ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
- ("ocaml-xmlm" ,ocaml4.01-xmlm)
- ("ocaml-mcl" ,ocaml4.01-mcl)
- ("ocaml-gsl" ,ocaml4.01-gsl)
- ("cddlib-src" ,(package-source cddlib))))
- (propagated-inputs
- `(("pplacer-scripts" ,pplacer-scripts)))
- (synopsis "Phylogenetic placement of biological sequences")
- (description
- "Pplacer places query sequences on a fixed reference phylogenetic tree
-to maximize phylogenetic likelihood or posterior probability according to a
-reference alignment. Pplacer is designed to be fast, to give useful
-information about uncertainty, and to offer advanced visualization and
-downstream analysis.")
- (home-page "http://matsen.fhcrc.org/pplacer")
- (license license:gpl3))))
-
-;; This package is installed alongside 'pplacer'. It is a separate package so
-;; that it can use the python-build-system for the scripts that are
-;; distributed alongside the main OCaml binaries.
-(define pplacer-scripts
- (package
- (inherit pplacer)
- (name "pplacer-scripts")
- (build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'enter-scripts-dir
- (lambda _ (chdir "scripts") #t))
- (replace 'check
- (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
- (add-after 'install 'wrap-executables
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (let ((path (string-append
- (assoc-ref inputs "hmmer") "/bin:"
- (assoc-ref inputs "infernal") "/bin")))
- (display path)
- (wrap-program (string-append bin "/refpkg_align.py")
- `("PATH" ":" prefix (,path))))
- (let ((path (string-append
- (assoc-ref inputs "hmmer") "/bin")))
- (wrap-program (string-append bin "/hrefpkg_query.py")
- `("PATH" ":" prefix (,path)))))
- #t)))))
- (inputs
- `(("infernal" ,infernal)
- ("hmmer" ,hmmer)))
- (propagated-inputs
- `(("python-biopython" ,python2-biopython)
- ("taxtastic" ,taxtastic)))
- (synopsis "Pplacer Python scripts")))
-
(define-public python2-pbcore
(package
(name "python2-pbcore")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
- version ".zip"))
+ (uri (pypi-uri "WarpedLMM" version ".zip"))
(sha256
(base32
"1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
(define-public star
(package
(name "star")
- (version "2.6.0c")
+ (version "2.7.0b")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "04cj6jw8d9q6lk9c78wa4fky6jdlicf1d13plq7182h8vqiz8p59"))
+ "1lih6cbpvnvhyvvswdhy06mwyzvwax96m723378v4z6psqzsh11d"))
(modules '((guix build utils)))
(snippet
'(begin
(("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
(string-append pre "Built with Guix" post)))
#t))
+ ;; See https://github.com/alexdobin/STAR/pull/562
+ (add-after 'enter-source-dir 'add-missing-header
+ (lambda _
+ (substitute* "SoloReadFeature_inputRecords.cpp"
+ (("#include \"binarySearch2.h\"" h)
+ (string-append h "\n#include <math.h>")))
+ #t))
(add-after 'enter-source-dir 'do-not-use-bundled-htslib
(lambda _
(substitute* "Makefile"
(supported-systems '("i686-linux" "x86_64-linux"))
(license license:bsd-3)))
+(define-public r-scde
+ (package
+ (name "r-scde")
+ (version "1.99.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/hms-dbmi/scde.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "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)))
+ (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
+analyzing single-cell RNA-seq data. SCDE fits individual error models for
+single-cell RNA-seq measurements. These models can then be used for
+assessment of differential expression between groups of cells, as well as
+other types of analysis. The SCDE package also contains the pagoda framework
+which applies pathway and gene set overdispersion analysis to identify aspects
+of transcriptional heterogeneity among single cells.")
+ ;; See https://github.com/hms-dbmi/scde/issues/38
+ (license license:gpl2)))
+
(define-public r-centipede
(package
(name "r-centipede")
information as possible.")
(license (list license:gpl2+ license:gpl3+))))
-(define-public r-vegan
- (package
- (name "r-vegan")
- (version "2.5-3")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "vegan" version))
- (sha256
- (base32
- "023xznh0iy0496icpchadmp7a3rk3nj9s48fvwlvp3dssw58yp3c"))))
- (build-system r-build-system)
- (native-inputs
- `(("gfortran" ,gfortran)))
- (propagated-inputs
- `(("r-cluster" ,r-cluster)
- ("r-knitr" ,r-knitr) ; needed for vignettes
- ("r-lattice" ,r-lattice)
- ("r-mass" ,r-mass)
- ("r-mgcv" ,r-mgcv)
- ("r-permute" ,r-permute)))
- (home-page "https://cran.r-project.org/web/packages/vegan")
- (synopsis "Functions for community ecology")
- (description
- "The vegan package provides tools for descriptive community ecology. It
-has most basic functions of diversity analysis, community ordination and
-dissimilarity analysis. Most of its multivariate tools can be used for other
-data types as well.")
- (license license:gpl2+)))
-
-(define-public r-annotate
- (package
- (name "r-annotate")
- (version "1.60.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "annotate" version))
- (sha256
- (base32
- "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-rcurl" ,r-rcurl)
- ("r-xml" ,r-xml)
- ("r-xtable" ,r-xtable)))
- (home-page
- "https://bioconductor.org/packages/annotate")
- (synopsis "Annotation for microarrays")
- (description "This package provides R environments for the annotation of
-microarrays.")
- (license license:artistic2.0)))
-
-(define-public r-copynumber
- (package
- (name "r-copynumber")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "copynumber" version))
- (sha256
- (base32
- "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-s4vectors" ,r-s4vectors)
- ("r-iranges" ,r-iranges)
- ("r-genomicranges" ,r-genomicranges)
- ("r-biocgenerics" ,r-biocgenerics)))
- (home-page "https://bioconductor.org/packages/copynumber")
- (synopsis "Segmentation of single- and multi-track copy number data")
- (description
- "This package segments single- and multi-track copy number data by a
-penalized least squares regression method.")
- (license license:artistic2.0)))
-
-(define-public r-geneplotter
- (package
- (name "r-geneplotter")
- (version "1.60.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "geneplotter" version))
- (sha256
- (base32
- "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-lattice" ,r-lattice)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
- (home-page "https://bioconductor.org/packages/geneplotter")
- (synopsis "Graphics functions for genomic data")
- (description
- "This package provides functions for plotting genomic data.")
- (license license:artistic2.0)))
-
(define-public r-genefilter
(package
(name "r-genefilter")
"This package provides a pipeline for the analysis of GRO-seq data.")
(license license:gpl3+)))
-(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
- (package
- (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
- (version "3.2.2")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/annotation/src/contrib"
- "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
- version ".tar.gz"))
- (sha256
- (base32
- "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
- (properties
- `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-genomicfeatures" ,r-genomicfeatures)))
- (home-page
- "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
- (synopsis "Annotation package for human genome in TxDb format")
- (description
- "This package provides an annotation database of Homo sapiens genome
-data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
-track. The database is exposed as a @code{TxDb} object.")
- (license license:artistic2.0)))
-
(define-public r-sparql
(package
(name "r-sparql")
barplots or heatmaps.")
(license license:gpl2+)))
-(define-public r-biocgenerics
- (package
- (name "r-biocgenerics")
- (version "0.28.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "BiocGenerics" version))
- (sha256
- (base32
- "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
- (properties
- `((upstream-name . "BiocGenerics")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/BiocGenerics")
- (synopsis "S4 generic functions for Bioconductor")
- (description
- "This package provides S4 generic functions needed by many Bioconductor
-packages.")
- (license license:artistic2.0)))
-
(define-public r-biocinstaller
(package
(name "r-biocinstaller")
(define-public r-optparse
(package
(name "r-optparse")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "optparse" version))
(sha256
(base32
- "1d7v5gl45x4amsfmzn5zyyffyqlc7a82h01szlnda22viyxids0h"))))
+ "04vyb6dhcga30mvghsg1p052jmf69xqxkvh3hzqz7dscyppy76w1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-getopt" ,r-getopt)))
that accept short and long options.")
(license license:gpl2+)))
-(define-public r-dnacopy
- (package
- (name "r-dnacopy")
- (version "1.56.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "DNAcopy" version))
- (sha256
- (base32
- "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
- (properties
- `((upstream-name . "DNAcopy")))
- (build-system r-build-system)
- (inputs
- `(("gfortran" ,gfortran)))
- (home-page "https://bioconductor.org/packages/DNAcopy")
- (synopsis "Implementation of a circular binary segmentation algorithm")
- (description "This package implements the circular binary segmentation (CBS)
-algorithm to segment DNA copy number data and identify genomic regions with
-abnormal copy number.")
- (license license:gpl2+)))
-
(define-public r-s4vectors
(package
(name "r-s4vectors")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.28.8")
+ (version "1.28.10")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "0gf36lr9xy3zmcc4rxs5bi2ccrrc7b6wqp6p3cvnclgif4i0l66k"))))
+ "0kxf583cgkdz1shi85r0mpnfxmzi7s5f6srd1czbdl2iibvrm8jn"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.42.0")
+ (version "1.42.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "0a4mhd926w9slkfil5xgngjsfdj024a4w57w2bm3d4r0pj8y5da7"))))
+ "1ycmcxvgvszvjv75hlmg0i6pq8i7r8720vgmfayb905s9l6j82x6"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.34.1")
+ (version "1.34.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0slq6hv5bmc3bgrl824jzmr6db3fvaj6b7ihwmdn76pgqqbq2fq6"))))
+ "0qs94b0ywrjyc9m1jykrbch3lb07576m508dikvx18vwn304mban"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
genome data packages and support for efficient SNP representation.")
(license license:artistic2.0)))
-(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
- (package
- (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
- (version "0.99.1")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.1000genomes.hs37d5_"
- version ".tar.gz"))
- (sha256
- (base32
- "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
- (properties
- `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
- (synopsis "Full genome sequences for Homo sapiens")
- (description
- "This package provides full genome sequences for Homo sapiens from
-1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
- (license license:artistic2.0)))
-
(define-public r-impute
(package
(name "r-impute")
Stephens (1990).")
(license license:lgpl2.0+)))
-(define-public r-bsgenome-hsapiens-ucsc-hg19
- (package
- (name "r-bsgenome-hsapiens-ucsc-hg19")
- (version "1.4.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.UCSC.hg19_"
- version ".tar.gz"))
- (sha256
- (base32
- "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
- (properties
- `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
- (synopsis "Full genome sequences for Homo sapiens")
- (description
- "This package provides full genome sequences for Homo sapiens as provided
-by UCSC (hg19, February 2009) and stored in Biostrings objects.")
- (license license:artistic2.0)))
-
-(define-public r-bsgenome-mmusculus-ucsc-mm9
- (package
- (name "r-bsgenome-mmusculus-ucsc-mm9")
- (version "1.4.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm9_"
- version ".tar.gz"))
- (sha256
- (base32
- "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
- (properties
- `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
- (synopsis "Full genome sequences for Mouse")
- (description
- "This package provides full genome sequences for Mus musculus (Mouse) as
-provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
- (license license:artistic2.0)))
-
-(define-public r-bsgenome-mmusculus-ucsc-mm10
- (package
- (name "r-bsgenome-mmusculus-ucsc-mm10")
- (version "1.4.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm10_"
- version ".tar.gz"))
- (sha256
- (base32
- "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
- (properties
- `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
- (synopsis "Full genome sequences for Mouse")
- (description
- "This package provides full genome sequences for Mus
-musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
-in Biostrings objects.")
- (license license:artistic2.0)))
-
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
based on the knownGene track.")
(license license:artistic2.0)))
-(define-public r-bsgenome-celegans-ucsc-ce6
- (package
- (name "r-bsgenome-celegans-ucsc-ce6")
- (version "1.4.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Celegans.UCSC.ce6_"
- version ".tar.gz"))
- (sha256
- (base32
- "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
- (properties
- `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
- (synopsis "Full genome sequences for Worm")
- (description
- "This package provides full genome sequences for Caenorhabditis
-elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
-objects.")
- (license license:artistic2.0)))
-
(define-public r-bsgenome-celegans-ucsc-ce10
(package
(name "r-bsgenome-celegans-ucsc-ce10")
(define-public r-qtl
(package
(name "r-qtl")
- (version "1.42-8")
+ (version "1.44-9")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6"))))
+ "03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i"))))
(build-system r-build-system)
(home-page "http://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
(define-public rcas-web
(package
(name "rcas-web")
- (version "0.0.5")
+ (version "0.1.0")
(source
(origin
(method url-fetch)
"/rcas-web-" version ".tar.gz"))
(sha256
(base32
- "0igz7jpcf7cm9800zcag6p3gd1i649figrhbdba6cjkm8f4gfspr"))))
+ "0wq951aj45gqki1bickg876i993lmawkp8x24agg264br5x716db"))))
(build-system gnu-build-system)
(arguments
`(#:phases
("r-rcas" ,r-rcas)
("guile-next" ,guile-2.2)
("guile-json" ,guile-json)
- ("guile-redis" ,guile2.2-redis)))
+ ("guile-redis" ,guile-redis)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://github.com/BIMSBbioinfo/rcas-web")
(version "1.0.9")
(source (origin
(method url-fetch)
- (uri (string-append "https://pypi.python.org/packages/source/P"
- "/PePr/PePr-" version ".tar.gz"))
+ (uri (pypi-uri "PePr" version))
(sha256
(base32
"0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
- (version "1.4.0")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SingleCellExperiment" version))
(sha256
(base32
- "19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj"))))
+ "12139kk9cqgzpm6f3cwdsq31gj5lxamz2q939dy9fa0fa54gdaq4"))))
(properties
`((upstream-name . "SingleCellExperiment")))
(build-system r-build-system)
(define-public r-scater
(package
(name "r-scater")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3"))))
+ "0rijhy7g5qmcn927y1wyd63la1fhyar9fv1hccsqd23jd98yc55a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
(native-inputs
`(("ldc" ,ldc)
("rdmd" ,rdmd)
- ("python" ,python-minimal)
+ ("python" ,python)
("biod"
,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
(origin
(define-public bismark
(package
(name "bismark")
- (version "0.19.1")
+ (version "0.20.1")
(source
(origin
(method git-fetch)
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
- (snippet
- '(begin
- ;; highcharts.js is non-free software. The code is available under
- ;; CC-BY-NC or proprietary licenses only.
- (delete-file "bismark_sitrep/highcharts.js")
- #t))))
+ "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9"))))
(build-system perl-build-system)
(arguments
`(#:tests? #f ; there are no tests
+ #:modules ((guix build utils)
+ (ice-9 popen)
+ (srfi srfi-26)
+ (guix build perl-build-system))
#:phases
(modify-phases %standard-phases
+ ;; The bundled plotly.js is minified.
+ (add-after 'unpack 'replace-plotly.js
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((file (assoc-ref inputs "plotly.js"))
+ (installed "plotly/plotly.js"))
+ (let ((minified (open-pipe* OPEN_READ "uglify-js" file)))
+ (call-with-output-file installed
+ (cut dump-port minified <>))))
+ #t))
(delete 'configure)
(delete 'build)
(replace 'install
"deduplicate_bismark"
"filter_non_conversion"
"bam2nuc"
- "bismark2summary")))
+ "bismark2summary"
+ "NOMe_filtering")))
(substitute* "bismark2report"
- (("\\$RealBin/bismark_sitrep")
- (string-append share "/bismark_sitrep")))
+ (("\\$RealBin/plotly")
+ (string-append share "/plotly")))
(mkdir-p share)
(mkdir-p docdir)
(mkdir-p bin)
(for-each (lambda (file) (install-file file docdir))
docs)
(copy-recursively "Docs/Images" (string-append docdir "/Images"))
- (copy-recursively "bismark_sitrep"
- (string-append share "/bismark_sitrep"))
+ (copy-recursively "plotly"
+ (string-append share "/plotly"))
;; Fix references to gunzip
(substitute* (map (lambda (file)
"/bin/gunzip -c")))
#t))))))
(inputs
- `(("gzip" ,gzip)))
+ `(("gzip" ,gzip)
+ ("perl-carp" ,perl-carp)
+ ("perl-getopt-long" ,perl-getopt-long)))
+ (native-inputs
+ `(("plotly.js"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/"
+ "v1.39.4/dist/plotly.js"))
+ (sha256
+ (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr"))))
+ ("uglify-js" ,uglify-js)))
(home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
(synopsis "Map bisulfite treated sequence reads and analyze methylation")
(description "Bismark is a program to map bisulfite treated sequencing
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
- (version "0.0.20")
+ (version "0.0.31")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
- "19a7dclqq0b4kqg3phiz4d4arlwfp34nm3z0rf1gkqdpsy7gghp3"))))
+ "0l3vd9xwqzap3mmyj8xwqp84kj7scbq308diqnwg2albphl75xqs"))))
(build-system gnu-build-system)
;; parts of the tests rely on access to the network
(arguments '(#:tests? #f))
HTML reports with interesting findings about your samples.")
(license license:gpl3+)))
+(define-public genrich
+ (package
+ (name "genrich")
+ (version "0.5")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jsh58/Genrich.git")
+ (commit (string-append "v" version))))
+ (sha256
+ (base32
+ "0x0q6z0208n3cxzqjla4rgjqpyqgwpmz27852lcvzkzaigymq4zp"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/jsh58/Genrich")
+ (synopsis "Detecting sites of genomic enrichment")
+ (description "Genrich is a peak-caller for genomic enrichment
+assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated
+following the assay and produces a file detailing peaks of significant
+enrichment.")
+ (license license:expat)))
+
(define-public mantis
(let ((commit "4ffd171632c2cb0056a86d709dfd2bf21bc69b84")
(revision "1"))
assembly, detect base modifications, call SNPs (Single nucleotide
polymorphisms) and indels with respect to a reference genome and more.")
(license license:expat))))
+
+(define-public cnvkit
+ (package
+ (name "cnvkit")
+ (version "0.9.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/etal/cnvkit.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (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)))
+ (home-page "https://cnvkit.readthedocs.org/")
+ (synopsis "Copy number variant detection from targeted DNA sequencing")
+ (description
+ "CNVkit is a Python library and command-line software toolkit to infer
+and visualize copy number from high-throughput DNA sequencing data. It is
+designed for use with hybrid capture, including both whole-exome and custom
+target panels, and short-read sequencing platforms such as Illumina and Ion
+Torrent.")
+ (license license:asl2.0)))
+
+(define-public python-pyfit-sne
+ (package
+ (name "python-pyfit-sne")
+ (version "1.0.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/KlugerLab/pyFIt-SNE.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "13wh3qkzs56azmmgnxib6xfr29g7xh09sxylzjpni5j0pp0rc5qw"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)))
+ (inputs
+ `(("fftw" ,fftw)))
+ (native-inputs
+ `(("python-cython" ,python-cython)))
+ (home-page "https://github.com/KlugerLab/pyFIt-SNE")
+ (synopsis "FFT-accelerated Interpolation-based t-SNE")
+ (description
+ "t-Stochastic Neighborhood Embedding (t-SNE) is a highly successful
+method for dimensionality reduction and visualization of high dimensional
+datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to
+approximate the gradient at each iteration of gradient descent. This package
+is a Cython wrapper for FIt-SNE.")
+ (license license:bsd-4)))
+
+(define-public velvet
+ (package
+ (name "velvet")
+ (version "1.2.10")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://www.ebi.ac.uk/~zerbino/velvet/"
+ "velvet_" version ".tgz"))
+ (sha256
+ (base32
+ "0h3njwy66p6bx14r3ar1byb0ccaxmxka4c65rn4iybyiqa4d8kc8"))
+ ;; Delete bundled libraries
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file "Manual.pdf")
+ (delete-file-recursively "third-party")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags '("OPENMP=t")
+ #:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'fix-zlib-include
+ (lambda _
+ (substitute* "src/binarySequences.c"
+ (("../third-party/zlib-1.2.3/zlib.h") "zlib.h"))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (doc (string-append out "/share/doc/velvet")))
+ (mkdir-p bin)
+ (mkdir-p doc)
+ (install-file "velveth" bin)
+ (install-file "velvetg" bin)
+ (install-file "Manual.pdf" doc)
+ (install-file "Columbus_manual.pdf" doc)
+ #t))))))
+ (inputs
+ `(("openmpi" ,openmpi)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("texlive" ,(texlive-union (list texlive-latex-graphics
+ texlive-latex-hyperref)))))
+ (home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
+ (synopsis "Nucleic acid sequence assembler for very short reads")
+ (description
+ "Velvet is a de novo genomic assembler specially designed for short read
+sequencing technologies, such as Solexa or 454. Velvet currently takes in
+short read sequences, removes errors then produces high quality unique
+contigs. It then uses paired read information, if available, to retrieve the
+repeated areas between contigs.")
+ (license license:gpl2+)))
HCoop / jackhill / guix / guix.git / blobdiff