From 909301591d21d3879276e4ede3cebdcc867184f2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 5 Jun 2018 15:42:23 +0200 Subject: gnu: Add sjcount. * gnu/packages/bioinformatics.scm (sjcount): New variable. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 122d6a740b..432589391b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13164,3 +13164,54 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) + +(define-public sjcount + ;; There is no tag for version 3.2, nor is there a release archive. + (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5") + (revision "1")) + (package + (name "sjcount") + (version (git-version "3.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pervouchine/sjcount-full.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; requires a 1.4G test file + #:make-flags + (list (string-append "SAMTOOLS_DIR=" + (assoc-ref %build-inputs "samtools") + "/lib/")) + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "makefile" + (("-I \\$\\{SAMTOOLS_DIR\\}") + (string-append "-I" (assoc-ref inputs "samtools") + "/include/samtools")) + (("-lz ") "-lz -lpthread ")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (for-each (lambda (tool) + (install-file tool + (string-append (assoc-ref outputs "out") + "/bin"))) + '("j_count" "b_count" "sjcount")) + #t))))) + (inputs + `(("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "https://github.com/pervouchine/sjcount-full/") + (synopsis "Annotation-agnostic splice junction counting pipeline") + (description "Sjcount is a utility for fast quantification of splice +junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This +version does count multisplits.") + (license license:gpl3+)))) -- cgit v1.2.3