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gnu: Add BLESS.

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* gnu/packages/bioinformatics.scm (bless): New variable.

Co-authored-by: Diane Trout <diane@ghic.org>
This commit is contained in:
Ricardo Wurmus 2015-11-06 15:22:26 +01:00
parent 00dfc97c36
commit 6c2b26e21e
1 changed files with 83 additions and 0 deletions
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83
gnu/packages/bioinformatics.scm
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@ -44,6 +44,7 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@ -524,6 +525,88 @@ confidence to have in an alignment.")
license:lgpl2.0+
license:asl2.0))))
(define-public bless
(package
(name "bless")
(version "1p02")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/bless-ec/bless.v"
version ".tgz"))
(sha256
(base32
"0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
(modules '((guix build utils)))
(snippet
`(begin
;; Remove bundled boost, pigz, zlib, and .git directory
;; FIXME: also remove bundled sources for google-sparsehash,
;; murmurhash3, kmc once packaged.
(delete-file-recursively "boost")
(delete-file-recursively "pigz")
(delete-file-recursively "zlib")
(delete-file-recursively ".git")
#t))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
#:make-flags
(list (string-append "ZLIB="
(assoc-ref %build-inputs "zlib")
"/lib/libz.a")
(string-append "LDFLAGS="
(string-join '("-lboost_filesystem"
"-lboost_system"
"-lboost_iostreams"
"-lz"
"-fopenmp"
"-std=c++11"))))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'do-not-build-bundled-pigz
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "Makefile"
(("cd pigz/pigz-2.3.3; make") ""))
#t))
(add-after 'unpack 'patch-paths-to-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "parse_args.cpp"
(("kmc_binary = .*")
(string-append "kmc_binary = \""
(assoc-ref outputs "out")
"/bin/kmc\";"))
(("pigz_binary = .*")
(string-append "pigz_binary = \""
(assoc-ref inputs "pigz")
"/bin/pigz\";")))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(for-each (lambda (file)
(install-file file bin))
'("bless" "kmc/bin/kmc"))
#t)))
(delete 'configure))))
(native-inputs
`(("perl" ,perl)))
(inputs
`(("openmpi" ,openmpi)
("boost" ,boost)
("pigz" ,pigz)
("zlib" ,zlib)))
(home-page "http://sourceforge.net/projects/bless-ec/wiki/Home/")
(synopsis "Bloom-filter-based error correction tool for NGS reads")
(description
"@dfn{Bloom-filter-based error correction solution for high-throughput
sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
correction tool for genomic reads produced by @dfn{Next-generation
sequencing} (NGS). BLESS produces accurate correction results with much less
memory compared with previous solutions and is also able to tolerate a higher
false-positive rate. BLESS can extend reads like DNA assemblers to correct
errors at the end of reads.")
(license license:gpl3+)))
(define-public bowtie
(package
(name "bowtie")