From b429c4fbb06299ce10ecc113a7818bf777c63a6e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 14 Sep 2015 16:32:27 +0200 Subject: gnu: Add bio-locus. * gnu/packages/bioinformatics.scm (bio-locus): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 03eb2dfe30..c4ba0e082f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2616,3 +2616,27 @@ (define-public vcftools ;; 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 fast database.") + (home-page "https://github.com/pjotrp/bio-locus") + (license license:expat))) -- cgit v1.2.3 From 801a0a221956dfeeddf7a8c85a66ff106dc33d7a Mon Sep 17 00:00:00 2001 From: David Thompson Date: Mon, 14 Sep 2015 12:05:15 -0400 Subject: Revert "gnu: Add bio-locus." This reverts commit b429c4fbb06299ce10ecc113a7818bf777c63a6e. --- gnu/packages/bioinformatics.scm | 24 ------------------------ 1 file changed, 24 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c4ba0e082f..03eb2dfe30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2616,27 +2616,3 @@ (define-public vcftools ;; 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 fast database.") - (home-page "https://github.com/pjotrp/bio-locus") - (license license:expat))) -- cgit v1.2.3 From 9c38b54027ee009f9ff604342ae99c4ebd7958a6 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 14 Sep 2015 16:32:27 +0200 Subject: gnu: Add bio-locus. * gnu/packages/bioinformatics.scm (bio-locus): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 03eb2dfe30..1f3421126c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -27,6 +27,7 @@ (define-module (gnu packages bioinformatics) #:use-module (guix build-system cmake) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system ruby) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages algebra) @@ -45,6 +46,7 @@ (define-module (gnu packages bioinformatics) #: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) @@ -2616,3 +2618,27 @@ (define-public vcftools ;; 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))) -- cgit v1.2.3 From 41ddebdd2a94da127369ab13fb1ccaf226b30a43 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 12 Sep 2015 22:10:20 +1000 Subject: gnu: Add mafft. * gnu/packages/bioinformatics.scm (mafft): New variable. --- gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f3421126c..a13fd7a91d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1545,6 +1545,64 @@ (define-public macs 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 -- cgit v1.2.3 From edb15985f1123e54199bac7228e49fb84371e0cb Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 17 Sep 2015 06:17:44 +0000 Subject: gnu: Add bioruby. * gnu/packages/bioinformatics.scm (bioruby): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a13fd7a91d..37bd3339d3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2700,3 +2700,46 @@ (define-public bio-locus 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+ )))) -- cgit v1.2.3 From a5002ae77c00693792ae0024b290cc24fb1d4328 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Sun, 20 Sep 2015 00:32:45 +0200 Subject: gnu: Add R/qtl. * gnu/packages/bioinformatics.scm (r-qtl): New variable. Co-authored-by: Pjotr Prins --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37bd3339d3..2e31d85b2d 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 ;;; Copyright © 2015 Ben Woodcroft +;;; Copyright © 2015 Pjotr Prins +;;; Copyright © 2015 Andreas Enge ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,6 +29,7 @@ (define-module (gnu packages bioinformatics) #: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) @@ -2743,3 +2746,28 @@ (define-public bioruby ;; 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))) -- cgit v1.2.3