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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-11-06 15:22:26 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-11-06 18:20:50 +0100
commit6c2b26e21eb95b48616aee1613bbf80d02e22495 (patch)
tree811affff431e54710614b50b34a15f1ae0ab461e /gnu/packages/bioinformatics.scm
parent00dfc97c36954307b4eb6ebfdbe7d3c238f5a874 (diff)
gnu: Add BLESS.
* gnu/packages/bioinformatics.scm (bless): New variable. Co-authored-by: Diane Trout <diane@ghic.org>
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm83
1 files changed, 83 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2e048bdabc..fe55e91a91 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")