diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 0 insertions, 42 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2073541ca5..2c5ad343f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4025,48 +4025,6 @@ standard linear mixed model resolver with application in @acronym{GWAS, genome-wide association studies}.") (license license:gpl3))) -(define-public grit - (package - (name "grit") - (version "2.0.5") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/nboley/grit") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'generate-from-cython-sources - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Delete these C files to force fresh generation from pyx sources. - (delete-file "grit/sparsify_support_fns.c") - (delete-file "grit/call_peaks_support_fns.c") - (substitute* "setup.py" - (("Cython.Setup") "Cython.Build")) - #t))))) - (inputs - (list python2-scipy python2-numpy python2-pysam python2-networkx)) - (native-inputs - (list python2-cython)) - ;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21. - (home-page "https://github.com/nboley/grit") - (synopsis "Tool for integrative analysis of RNA-seq type assays") - (description - "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify -full length transcript models. When none of these data sources are available, -GRIT can be run by providing a candidate set of TES or TSS sites. In -addition, GRIT can merge in reference junctions and gene boundaries. GRIT can -also be run in quantification mode, where it uses a provided GTF file and just -estimates transcript expression.") - (license license:gpl3+))) - (define-public hisat (package (name "hisat") |