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-rw-r--r--gnu/packages/bioinformatics.scm155
1 files changed, 155 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bbd02f3123..1977fd3bf9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,6 +1,8 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -27,6 +29,8 @@
#:use-module (guix build-system cmake)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
+ #:use-module (guix build-system r)
+ #:use-module (guix build-system ruby)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
@@ -45,6 +49,7 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
@@ -1539,6 +1544,64 @@ resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
(license license:bsd-3)))
+(define-public mafft
+ (package
+ (name "mafft")
+ (version "7.221")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://mafft.cbrc.jp/alignment/software/mafft-" version
+ "-without-extensions-src.tgz"))
+ (file-name (string-append name "-" version ".tgz"))
+ (sha256
+ (base32
+ "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no automated tests, though there are tests in the read me
+ #:make-flags (let ((out (assoc-ref %outputs "out")))
+ (list (string-append "PREFIX=" out)
+ (string-append "BINDIR="
+ (string-append out "/bin"))))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "core") #t))
+ (add-after 'enter-dir 'patch-makefile
+ (lambda _
+ ;; on advice from the MAFFT authors, there is no need to
+ ;; distribute mafft-profile, mafft-distance, or
+ ;; mafft-homologs.rb as they are too "specialised".
+ (substitute* "Makefile"
+ ;; remove mafft-homologs.rb from SCRIPTS
+ (("^SCRIPTS = mafft mafft-homologs.rb")
+ "SCRIPTS = mafft")
+ ;; remove mafft-distance from PROGS
+ (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
+ "PROGS = dvtditr dndfast7 dndblast sextet5")
+ ;; remove mafft-profile from PROGS
+ (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
+ "splittbfast disttbfast tbfast f2cl mccaskillwrap")
+ (("^rm -f mafft-profile mafft-profile.exe") "#")
+ (("^rm -f mafft-distance mafft-distance.exe") ")#")
+ ;; do not install MAN pages in libexec folder
+ (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
+\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
+ #t))
+ (delete 'configure))))
+ (inputs
+ `(("perl" ,perl)))
+ (home-page "http://mafft.cbrc.jp/alignment/software/")
+ (synopsis "Multiple sequence alignment program")
+ (description
+ "MAFFT offers a range of multiple alignment methods for nucleotide and
+protein sequences. For instance, it offers L-INS-i (accurate; for alignment
+of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
+sequences).")
+ (license (license:non-copyleft
+ "http://mafft.cbrc.jp/alignment/software/license.txt"
+ "BSD-3 with different formatting"))))
(define-public metabat
(package
@@ -2607,3 +2670,95 @@ data in the form of VCF files.")
;; The license is declared as LGPLv3 in the README and
;; at http://vcftools.sourceforge.net/license.html
(license license:lgpl3)))
+
+(define-public bio-locus
+ (package
+ (name "bio-locus")
+ (version "0.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-locus" version))
+ (sha256
+ (base32
+ "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
+ (build-system ruby-build-system)
+ (native-inputs
+ `(("ruby-rspec" ,ruby-rspec)))
+ (synopsis "Tool for fast querying of genome locations")
+ (description
+ "Bio-locus is a tabix-like tool for fast querying of genome
+locations. Many file formats in bioinformatics contain records that
+start with a chromosome name and a position for a SNP, or a start-end
+position for indels. Bio-locus allows users to store this chr+pos or
+chr+pos+alt information in a database.")
+ (home-page "https://github.com/pjotrp/bio-locus")
+ (license license:expat)))
+
+(define-public bioruby
+ (package
+ (name "bioruby")
+ (version "1.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio" version))
+ (sha256
+ (base32
+ "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"))))
+ (build-system ruby-build-system)
+ (propagated-inputs
+ `(("ruby-libxml" ,ruby-libxml)))
+ (native-inputs
+ `(("which" ,which))) ; required for test phase
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'patch-test-command
+ (lambda _
+ (substitute* '("test/functional/bio/test_command.rb")
+ (("/bin/sh") (which "sh")))
+ (substitute* '("test/functional/bio/test_command.rb")
+ (("/bin/ls") (which "ls")))
+ (substitute* '("test/functional/bio/test_command.rb")
+ (("which") (which "which")))
+ (substitute* '("test/functional/bio/test_command.rb",
+ "test/data/command/echoarg2.sh")
+ (("/bin/echo") (which "echo")))
+ #t)))))
+ (synopsis "Ruby library, shell and utilities for bioinformatics")
+ (description "BioRuby comes with a comprehensive set of Ruby development
+tools and libraries for bioinformatics and molecular biology. BioRuby has
+components for sequence analysis, pathway analysis, protein modelling and
+phylogenetic analysis; it supports many widely used data formats and provides
+easy access to databases, external programs and public web services, including
+BLAST, KEGG, GenBank, MEDLINE and GO.")
+ (home-page "http://bioruby.org/")
+ ;; Code is released under Ruby license, except for setup
+ ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
+ (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
+
+(define-public r-qtl
+ (package
+ (name "r-qtl")
+ (version "1.37-11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/qtl_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi"))))
+ (build-system r-build-system)
+ (home-page "http://rqtl.org/")
+ (synopsis "R package for analyzing QTL experiments in genetics")
+ (description "R/qtl is an extension library for the R statistics
+system. It is used to analyze experimental crosses for identifying
+genes contributing to variation in quantitative traits (so-called
+quantitative trait loci, QTLs).
+
+Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
+identify genotyping errors, and to perform single-QTL and two-QTL,
+two-dimensional genome scans.")
+ (license license:gpl3)))