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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-10-14 22:37:54 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-10-14 22:49:04 +0200 |
| commit | 19e42618376e92cb9745197642ff5cb4afa39945 (patch) | |
| tree | 2e9f75738ef5655d348a7a95fcee012983b695f8 | |
| parent | dc505e3eb88faf3c952aa1de4a12a42111c3742c (diff) | |
| download | patches-19e42618376e92cb9745197642ff5cb4afa39945.tar patches-19e42618376e92cb9745197642ff5cb4afa39945.tar.gz | |
gnu: Add methyldackel.
* gnu/packages/bioinformatics.scm (methyldackel): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 44 insertions, 0 deletions
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))) |