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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2019-02-12 13:10:26 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-02-12 15:41:02 +0100 |
| commit | 385d7546e1e8fa3488cc2da07ad5d00a33e8d6c8 (patch) | |
| tree | 46a18afed0af8650d5888792a394db9aa3280972 /gnu/packages/bioinformatics.scm | |
| parent | c18dccffa20bf09826758210d457d1df477f959c (diff) | |
| download | patches-385d7546e1e8fa3488cc2da07ad5d00a33e8d6c8.tar patches-385d7546e1e8fa3488cc2da07ad5d00a33e8d6c8.tar.gz | |
gnu: Add cnvkit.
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02cafb2358..279d52ae98 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14441,3 +14441,39 @@ Nanopolish can calculate an improved consensus sequence for a draft genome 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))) |