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-rw-r--r--gnu/packages/bioinformatics.scm58
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