diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 000000000000..c7b71288fa90 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.3.0' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 000000000000..79449c632cff --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PerlModule' + +name = 'PSORTb' +version = '3.0.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://psort.org/psortb/index.html' +description = """PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.psort.org/download/'] +sources = ['bio-tools-psort-all.%(version)s.tar.gz'] + +patches = [ + 'PSORTb-%(version)s-libpsortb.patch', +] + +dependencies = [ + ('Perl', '5.22.1'), + ('libpsortb','1.0'), + ('BioPerl','1.6.924','-Perl-5.22.1'), + ('BLAST','2.2.26', '-Linux_x86_64', True), + ('pftoolsV3','20160324'), +] + +options = {'modulename': 'Bio::Tools::PSort'} + +preconfigopts = "export PSORTROOT=%(installdir)s && " + +prebuildopts = 'sed -i "s/CC = cc/CC ?= gcc/" bio-tools-psort-modhmm/Makefile && ' + +postinstallcmds = [ + "cp -r psort/* %(installdir)s/.", +] + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch new file mode 100644 index 000000000000..bbc5e91be1d4 --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch @@ -0,0 +1,130 @@ +Removed q and a and perl scripting environment set accordingly. +Author: Fokke Dijkstra (University of Groningen) +diff -ru bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm +--- bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm 2010-07-29 00:12:43.000000000 +0200 ++++ bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm 2015-11-26 13:50:18.000000000 +0100 +@@ -77,7 +77,12 @@ + } + } + } else { +- $input = ExtUtils::MakeMaker::prompt("\n$lib was not found in the dynamic linker path, is there somewhere else we should check? ", "/usr/local/lib$sixtyfour"); ++ if (exists($ENV{EBROOTLIBPSORTB})) { ++ $input = "$ENV{EBROOTLIBPSORTB}/lib$sixtyfour"; ++ } else { ++ $input = "/usr/local/lib$sixtyfour"; ++ } ++ $input = ExtUtils::MakeMaker::prompt("\n$lib was not found in the dynamic linker path, is there somewhere else we should check? ", $input); + if($path = Bio::Tools::PSort::Install->findLib("-L$input -l$lib")) { + $passed = 1; + $libpath = $input; +diff -ru bio-tools-psort-all/Makefile.PL bio-tools-psort-all.new/Makefile.PL +--- bio-tools-psort-all/Makefile.PL 2010-07-28 23:40:19.000000000 +0200 ++++ bio-tools-psort-all.new/Makefile.PL 2015-11-30 12:03:14.000000000 +0100 +@@ -97,7 +97,12 @@ + } + + sub get_psort_root { +- my $root = prompt("Where do you plan to install the psort configuration files?", '/usr/local/psortb'); ++ if(exists($ENV{PSORTROOT})) { ++ $root = $ENV{PSORTROOT}; ++ } else { ++ $root = '/usr/local/psortb'; ++ } ++ my $root = prompt("Where do you plan to install the psort configuration files?", $root); + $PSORT_ROOT = $root; + } + +Only in bio-tools-psort-all: .Makefile.PL.swp +diff -ru bio-tools-psort-all/psort/bin/check-sig bio-tools-psort-all.new/psort/bin/check-sig +--- bio-tools-psort-all/psort/bin/check-sig 2003-07-25 18:48:03.000000000 +0200 ++++ bio-tools-psort-all.new/psort/bin/check-sig 2015-11-26 13:51:19.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/bin/psort bio-tools-psort-all.new/psort/bin/psort +--- bio-tools-psort-all/psort/bin/psort 2010-05-26 23:51:55.000000000 +0200 ++++ bio-tools-psort-all.new/psort/bin/psort 2015-11-26 13:50:58.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Bio::Tools::PSort::Report::Formatter; + use Bio::Tools::PSort; +diff -ru bio-tools-psort-all/psort/bin/psort.tmpt bio-tools-psort-all.new/psort/bin/psort.tmpt +--- bio-tools-psort-all/psort/bin/psort.tmpt 2009-11-10 22:46:09.000000000 +0100 ++++ bio-tools-psort-all.new/psort/bin/psort.tmpt 2015-11-26 13:51:01.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Bio::Tools::PSort::Report::Formatter; + use Bio::Tools::PSort; +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/archaea/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/archaea/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/archaea/check-sig 2008-10-01 18:57:37.000000000 +0200 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/archaea/check-sig 2015-11-26 13:52:00.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/gramneg/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/gramneg/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/gramneg/check-sig 2004-02-25 08:50:44.000000000 +0100 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/gramneg/check-sig 2015-11-26 13:52:02.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/grampos/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/grampos/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/grampos/check-sig 2004-04-02 20:23:28.000000000 +0200 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/grampos/check-sig 2015-11-26 13:52:05.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/server/rpc/classify.xpl bio-tools-psort-all.new/psort/server/rpc/classify.xpl +--- bio-tools-psort-all/psort/server/rpc/classify.xpl 2004-03-05 20:47:06.000000000 +0100 ++++ bio-tools-psort-all.new/psort/server/rpc/classify.xpl 2015-11-26 13:52:20.000000000 +0100 +@@ -14,7 +14,7 @@ + + +