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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-05-28 17:33:37 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-05-28 23:00:47 +0200 |
| commit | b1ae0f30d856503fa311d380584a6d7c80559332 (patch) | |
| tree | e776bbebaca1578b39dcee6f9fcbc422c3b67fbc | |
| parent | 0b70eb03cbcf5df7de9f468d9e2a3b53379779fe (diff) | |
| download | guix-patches-b1ae0f30d856503fa311d380584a6d7c80559332.tar guix-patches-b1ae0f30d856503fa311d380584a6d7c80559332.tar.gz | |
gnu: Add mosaicatcher.
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38c0c07ef..2a7443314a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,6 +6170,46 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) +(define-public mosaicatcher + (package + (name "mosaicatcher") + (version "0.3.1") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/friendsofstrandseq/mosaicatcher") + (commit (string-append version "-dev")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) + (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #false ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((target (assoc-ref outputs "out")) + (bin (string-append target "/bin")) + (share (string-append target "/share/mosaicatcher"))) + (install-file "mosaic" bin) + (mkdir-p share) + (copy-recursively "../R" share))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib))) + (home-page "https://github.com/friendsofstrandseq/mosaicatcher") + (synopsis "Count and classify Strand-seq reads") + (description + "Mosaicatcher counts Strand-seq reads and classifies strand states of +each chromosome in each cell using a Hidden Markov Model.") + (license license:expat))) + (define-public ngs-sdk (package (name "ngs-sdk") |