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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-02-26 16:34:49 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-03-02 17:23:56 +0100 |
| commit | 191c710139af3e833f32b24ce1f225c344620bb3 (patch) | |
| tree | 5a6e3883c834857258a087b12e98ac4487a8f929 /gnu/packages/bioinformatics.scm | |
| parent | 1385d37a6e8b1218d38a57d08ee654a7ec8f6b21 (diff) | |
gnu: Add crossmap.
* gnu/packages/bioinformatics.scm (crossmap): New variable.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index de25f8c7b5..0960329f44 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -272,6 +272,48 @@ gapped, local, and paired-end alignment modes.") "CLIPper is a tool to define peaks in CLIP-seq datasets.") (license license:gpl2))) +(define-public crossmap + (package + (name "crossmap") + (version "0.1.6") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" + version ".tar.gz")) + (sha256 + (base32 + "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp")) + ;; patch has been sent upstream already + (patches (list + (search-patch "crossmap-allow-system-pysam.patch"))) + (modules '((guix build utils))) + ;; remove bundled copy of pysam + (snippet + '(delete-file-recursively "lib/pysam")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (alist-cons-after + 'unpack 'set-env + (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1")) + %standard-phases))) + (inputs + `(("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("zlib" ,zlib))) + (native-inputs + `(("python-cython" ,python2-cython) + ("python-nose" ,python2-nose) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://crossmap.sourceforge.net/") + (synopsis "Convert genome coordinates between assemblies") + (description + "CrossMap is a program for conversion of genome coordinates or annotation +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 flexbar (package (name "flexbar") |