diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 88 |
1 files changed, 87 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ca8dcb761a..3725f3ffe5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19,6 +19,7 @@ (define-module (gnu packages bioinformatics) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) @@ -401,6 +402,46 @@ files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) +(define-public cutadapt + (package + (name "cutadapt") + (version "1.8") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/marcelm/cutadapt/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5")))) + (build-system python-build-system) + (arguments + ;; tests must be run after install + `(#:phases (alist-cons-after + 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "PYTHONPATH" + (string-append + (getenv "PYTHONPATH") + ":" (assoc-ref outputs "out") + "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") 5) 3) + "/site-packages")) + (zero? (system* "nosetests" "-P" "tests"))) + (alist-delete 'check %standard-phases)))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools))) + (home-page "https://code.google.com/p/cutadapt/") + (synopsis "Remove adapter sequences from nucleotide sequencing reads") + (description + "Cutadapt finds and removes adapter sequences, primers, poly-A tails and +other types of unwanted sequence from high-throughput sequencing reads.") + (license license:expat))) + (define-public flexbar (package (name "flexbar") @@ -709,20 +750,25 @@ files and writing bioinformatics applications.") (chdir "pbtranscript-tofu/pbtranscript/") ;; Delete clutter (delete-file-recursively "dist/") + (delete-file-recursively "build/") (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/") (delete-file-recursively "pbtools.pbtranscript.egg-info") (delete-file "Cython-0.20.1.tar.gz") (delete-file "setuptools_cython-0.2.1-py2.7.egg") (delete-file "setuptools_cython-0.2.1.tar.gz") (delete-file "setup.cfg") + (for-each delete-file + (find-files "." "\\.so$")) ;; files should be writable for install phase (for-each (lambda (f) (chmod f #o755)) - (find-files "." "\\.py"))) + (find-files "." "\\.py$"))) %standard-phases))) (inputs `(("python-cython" ,python2-cython) ("python-numpy" ,python2-numpy) ("python-bx-python" ,python2-bx-python) + ("python-networkx" ,python2-networkx) + ("python-scipy" ,python2-scipy) ("python-pbcore" ,python2-pbcore))) (native-inputs `(("python-nose" ,python2-nose) @@ -929,3 +975,43 @@ chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.") ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. (license license:gpl3+))) + +(define-public vcftools + (package + (name "vcftools") + (version "0.1.12b") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/vcftools/vcftools_" + version ".tar.gz")) + (sha256 + (base32 + "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no "check" target + #:make-flags (list + (string-append "PREFIX=" (assoc-ref %outputs "out")) + (string-append "MANDIR=" (assoc-ref %outputs "out") + "/share/man/man1")) + #:phases + (alist-cons-after + 'unpack 'patch-manpage-install + (lambda _ + (substitute* "Makefile" + (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1"))) + (alist-delete 'configure %standard-phases)))) + (inputs + `(("perl" ,perl) + ("zlib" ,zlib))) + (home-page "http://vcftools.sourceforge.net/") + (synopsis "Tools for working with VCF files") + (description + "VCFtools is a program package designed for working with VCF files, such +as those generated by the 1000 Genomes Project. The aim of VCFtools is to +provide easily accessible methods for working with complex genetic variation +data in the form of VCF files.") + ;; The license is declared as LGPLv3 in the README and + ;; at http://vcftools.sourceforge.net/license.html + (license license:lgpl3))) |