ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-12-26 22:38:07 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions

gnu: seqan: Update to 2.4.0.

Browse source 
* gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0.
[native-inputs]: Replace bzip2 with xz.
(seqan-1): New variable.
(tophat)[inputs]: Use seqan-1.
This commit is contained in:
Ricardo Wurmus 2018-10-21 23:03:57 +02:00
parent 4b8f4536ce
commit 4d93a9a36c
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 47 additions and 11 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

58
gnu/packages/bioinformatics.scm
View file

@ -1382,7 +1382,7 @@ (define-public tophat
("python" ,python-2)
("perl" ,perl)
("zlib" ,zlib)
("seqan" ,seqan)))
("seqan" ,seqan-1)))
(home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
(synopsis "Spliced read mapper for RNA-Seq data")
(description
@ -5732,6 +5732,51 @@ (define-public sra-tools
(define-public seqan
(package
(name "seqan")
(version "2.4.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/seqan/seqan/releases/"
"download/seqan-v" version
"/seqan-library-" version ".tar.xz"))
(sha256
(base32
"19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx"))))
;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
;; makes sense to split the outputs.
(outputs '("out" "doc"))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils))
(let ((tar (assoc-ref %build-inputs "tar"))
(xz (assoc-ref %build-inputs "xz"))
(out (assoc-ref %outputs "out"))
(doc (assoc-ref %outputs "doc")))
(setenv "PATH" (string-append tar "/bin:" xz "/bin"))
(invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
(chdir (string-append "seqan-library-" ,version))
(copy-recursively "include" (string-append out "/include"))
(copy-recursively "share" (string-append doc "/share"))
#t))))
(native-inputs
`(("source" ,source)
("tar" ,tar)
("xz" ,xz)))
(home-page "http://www.seqan.de")
(synopsis "Library for nucleotide sequence analysis")
(description
"SeqAn is a C++ library of efficient algorithms and data structures for
the analysis of sequences with the focus on biological data. It contains
algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
(define-public seqan-1
(package (inherit seqan)
(name "seqan")
(version "1.4.2")
(source (origin
@ -5763,16 +5808,7 @@ (define-public seqan
(native-inputs
`(("source" ,source)
("tar" ,tar)
("bzip2" ,bzip2)))
(home-page "http://www.seqan.de")
(synopsis "Library for nucleotide sequence analysis")
(description
"SeqAn is a C++ library of efficient algorithms and data structures for
the analysis of sequences with the focus on biological data. It contains
algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
("bzip2" ,bzip2)))))
(define-public seqmagick
(package