diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 83 |
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") |