diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 144 |
1 files changed, 144 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6df298db5..8ed871003a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -143,6 +143,39 @@ intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.") (license license:gpl2))) +(define-public python2-pybedtools + (package + (name "python2-pybedtools") + (version "0.6.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" + version ".tar.gz")) + (sha256 + (base32 + "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; no Python 3 support + (inputs + `(("python-cython" ,python2-cython) + ("python-matplotlib" ,python2-matplotlib))) + (propagated-inputs + `(("bedtools" ,bedtools) + ("samtools" ,samtools))) + (native-inputs + `(("python-pyyaml" ,python2-pyyaml) + ("python-nose" ,python2-nose) + ("python-setuptools" ,python2-setuptools))) + (home-page "https://pythonhosted.org/pybedtools/") + (synopsis "Python wrapper for BEDtools programs") + (description + "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, +which are widely used for genomic interval manipulation or \"genome algebra\". +pybedtools extends BEDTools by offering feature-level manipulations from with +Python.") + (license license:gpl2+))) + (define-public bowtie (package (name "bowtie") @@ -204,6 +237,86 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public clipper + (package + (name "clipper") + (version "0.3.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/YeoLab/clipper/archive/" + version ".tar.gz")) + (sha256 + (base32 + "1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq")) + (modules '((guix build utils))) + (snippet + ;; remove unnecessary setup dependency + '(substitute* "setup.py" + (("setup_requires = .*") ""))))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; only Python 2 is supported + (inputs + `(("htseq" ,htseq) + ("python-pybedtools" ,python2-pybedtools) + ("python-cython" ,python2-cython) + ("python-scikit-learn" ,python2-scikit-learn) + ("python-matplotlib" ,python2-matplotlib) + ("python-pysam" ,python2-pysam) + ("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))) + (home-page "https://github.com/YeoLab/clipper") + (synopsis "CLIP peak enrichment recognition") + (description + "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") @@ -333,6 +446,37 @@ particular, reads spanning multiple exons.") from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public macs + (package + (name "macs") + (version "2.1.0.20140616") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/M/MACS2/MACS2-" + version ".tar.gz")) + (sha256 + (base32 + "11lmiw6avqhwn75sn59g4lfkrr2kk20r3rgfbx9xfqb8rg9mi2n6")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; only compatible with Python 2.7 + #: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 + "MACS is an implementation of a ChIP-Seq analysis algorithm for +identifying transcript factor binding sites named Model-based Analysis of +ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate +the significance of enriched ChIP regions and it improves the spatial +resolution of binding sites through combining the information of both +sequencing tag position and orientation.") + (license license:bsd-3))) + (define-public rseqc (package (name "rseqc") |