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branch master updated: gnu: Add segemehl.
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guix-commits |
Subject: |
branch master updated: gnu: Add segemehl. |
Date: |
Mon, 26 Jul 2021 05:10:33 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 99ca1ae gnu: Add segemehl.
99ca1ae is described below
commit 99ca1ae4f852387ea0db16a9143726ff9b5a3f84
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Jul 26 11:07:56 2021 +0200
gnu: Add segemehl.
* gnu/packages/bioinformatics.scm (segemehl): New variable.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a90a7fa..91a3c1f 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")
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