diff options
Diffstat (limited to 'gnu/packages')
| -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))) |