diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 55 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0d8a6d518c..12c9175ed3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,6 +29,7 @@ #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages boost) #:use-module (gnu packages compression) @@ -87,7 +89,7 @@ BAM files.") (define-public bedops (package (name "bedops") - (version "2.4.5") + (version "2.4.14") (source (origin (method url-fetch) (uri (string-append "https://github.com/bedops/bedops/archive/v" @@ -95,7 +97,7 @@ BAM files.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5")))) + "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) (build-system gnu-build-system) (arguments '(#:tests? #f @@ -615,6 +617,56 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") other types of unwanted sequence from high-throughput sequencing reads.") (license license:expat))) +(define-public diamond + (package + (name "diamond") + (version "0.7.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/bbuchfink/diamond/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15")) + (snippet '(begin + (delete-file "bin/diamond") + #t)))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-source-dir + (lambda _ + (chdir "src") + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (copy-file "../bin/diamond" + (string-append bin "/diamond")) + #t)))))) + (native-inputs + `(("bc" ,bc))) + (inputs + `(("boost" ,boost) + ("zlib" ,zlib))) + (home-page "https://github.com/bbuchfink/diamond") + (synopsis "Accelerated BLAST compatible local sequence aligner") + (description + "DIAMOND is a BLAST-compatible local aligner for mapping protein and +translated DNA query sequences against a protein reference database (BLASTP +and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short +reads at a typical sensitivity of 90-99% relative to BLAST depending on the +data and settings.") + (license (license:non-copyleft "file://src/COPYING" + "See src/COPYING in the distribution.")))) + (define-public edirect (package (name "edirect") @@ -1063,7 +1115,7 @@ sequencing tag position and orientation.") (source (origin (method url-fetch) (uri (string-append - "http://pypi.python.org/packages/source/m/misopy/misopy-" + "https://pypi.python.org/packages/source/m/misopy/misopy-" version ".tar.gz")) (sha256 (base32 |