From 19e42618376e92cb9745197642ff5cb4afa39945 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 14 Oct 2019 22:37:54 +0200 Subject: gnu: Add methyldackel. * gnu/packages/bioinformatics.scm (methyldackel): New variable. --- gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 12c30236cb..5f57a59b06 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15304,3 +15304,47 @@ pairs.") transcriptional derivatives and visualization of the resulting velocity patterns.") (license license:gpl3)))) + +(define-public methyldackel + (package + (name "methyldackel") + (version "0.4.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dpryan79/MethylDackel.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags + (list "CC=gcc" + (string-append "prefix=" + (assoc-ref %outputs "out") "/bin/")) + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("install MethylDackel \\$\\(prefix\\)" match) + (string-append "install -d $(prefix); " match))) + #t))))) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + ;; Needed for tests + (native-inputs + `(("python" ,python-wrapper))) + (home-page "https://github.com/dpryan79/MethylDackel") + (synopsis "Universal methylation extractor for BS-seq experiments") + (description + "MethylDackel will process a coordinate-sorted and indexed BAM or CRAM +file containing some form of BS-seq alignments and extract per-base +methylation metrics from them. MethylDackel requires an indexed fasta file +containing the reference genome as well.") + ;; See https://github.com/dpryan79/MethylDackel/issues/85 + (license license:expat))) -- cgit 1.4.1