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gnu: Add sra-tools.

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* gnu/packages/bioinformatics.scm (sra-tools): New variable.
This commit is contained in:
Ricardo Wurmus 2015-04-14 14:43:32 +02:00
parent 75dd242480
commit 51c649992e
1 changed files with 76 additions and 0 deletions
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76
gnu/packages/bioinformatics.scm
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@ -31,6 +31,7 @@ (define-module (gnu packages bioinformatics)
#:use-module (gnu packages compression)
#:use-module (gnu packages file)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
@ -1219,6 +1220,81 @@ (define-public ncbi-vdb
accessed/downloaded on demand across HTTP.")
(license license:public-domain)))
(define-public sra-tools
(package
(name "sra-tools")
(version "2.4.5-5")
(source
(origin
(method url-fetch)
(uri
(string-append "https://github.com/ncbi/sra-tools/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:phases
(alist-replace
'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
;; The build system expects a directory containing the sources and
;; raw build output of ncbi-vdb, including files that are not
;; installed. Since we are building against an installed version of
;; ncbi-vdb, the following modifications are needed.
(substitute* "setup/konfigure.perl"
;; Make the configure script look for the "ilib" directory of
;; "ncbi-vdb" without first checking for the existence of a
;; matching library in its "lib" directory.
(("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
"my $f = File::Spec->catdir($ilibdir, $ilib);")
;; Look for interface libraries in ncbi-vdb's "ilib" directory.
(("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
"my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system*
"./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug")
(string-append "--with-fuse-prefix="
(assoc-ref inputs "fuse"))
(string-append "--with-magic-prefix="
(assoc-ref inputs "libmagic"))
;; TODO: building with libxml2 fails with linker errors
;; (string-append "--with-xml2-prefix="
;; (assoc-ref inputs "libxml2"))
(string-append "--with-ncbi-vdb-sources="
(assoc-ref inputs "ncbi-vdb"))
(string-append "--with-ncbi-vdb-build="
(assoc-ref inputs "ncbi-vdb"))
(string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk"))
(string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5")))))
%standard-phases)))
(native-inputs `(("perl" ,perl)))
(inputs
`(("ngs-sdk" ,ngs-sdk)
("ncbi-vdb" ,ncbi-vdb)
("libmagic" ,file)
("fuse" ,fuse)
("hdf5" ,hdf5)
("zlib" ,zlib)))
(home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
(synopsis "Tools and libraries for reading and writing sequencing data")
(description
"The SRA Toolkit from NCBI is a collection of tools and libraries for
reading of sequencing files from the Sequence Read Archive (SRA) database and
writing files into the .sra format.")
(license license:public-domain)))
(define-public seqan
(package
(name "seqan")