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author | Ricardo Wurmus <rekado@elephly.net> | 2021-07-26 11:07:56 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2021-07-26 11:08:13 +0200 |
commit | 99ca1ae4f852387ea0db16a9143726ff9b5a3f84 (patch) | |
tree | e3c5b3057bff8d703b9b52d6e3d55d55f6a57eb0 /gnu | |
parent | d16694b546e86d8e3b0907e2a82a20790c33e9e5 (diff) | |
download | guix-patches-99ca1ae4f852387ea0db16a9143726ff9b5a3f84.tar guix-patches-99ca1ae4f852387ea0db16a9143726ff9b5a3f84.tar.gz |
gnu: Add segemehl.
* gnu/packages/bioinformatics.scm (segemehl): New variable.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a90a7fa9d4..91a3c1f185 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9388,6 +9388,54 @@ using nucleotide or amino-acid sequence data.") ;; GPLv3 only (license license:gpl3))) +(define-public segemehl + (package + (name "segemehl") + (version "0.3.4") + (source (origin + (method url-fetch) + (uri (string-append "https://www.bioinf.uni-leipzig.de/Software" + "/segemehl/downloads/segemehl-" + version ".tar.gz")) + (sha256 + (base32 + "0lbzbb7i8zadsn9b99plairhq6s2h1z8qdn6n7djclfis01nycz4")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + (list (string-append "CC=" ,(cc-for-target)) + "all") + #:tests? #false ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (exes (list "segemehl.x" "haarz.x"))) + (mkdir-p bin) + (for-each (lambda (exe) + (install-file exe bin)) + exes))))))) + (inputs + `(("htslib" ,htslib) + ("ncurses" ,ncurses) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://www.bioinf.uni-leipzig.de/Software/segemehl") + (synopsis "Map short sequencer reads to reference genomes") + (description "Segemehl is software to map short sequencer reads to +reference genomes. Segemehl implements a matching strategy based on enhanced +suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and +bgzip'ed). In addition to the alignment of reads from standard DNA- and +RNA-seq protocols, it also allows the mapping of bisulfite converted +reads (Lister and Cokus) and implements a split read mapping strategy. The +output of segemehl is a SAM or BAM formatted alignment file.") + (license license:gpl3+))) + (define-public kallisto (package (name "kallisto") |