easybuilders · boegel · Aug 30, 2016 · Jul 10, 2016 · Jul 10, 2016 · Jul 10, 2016
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
@@ -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 <fotis@cern.ch>, 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
@@ -0,0 +1,41 @@
+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+','2.3.0', '-Python-2.7.11'),
+    ('pftools','2.3'),
+]
+
+options = {'modulename': 'Bio::Tools::PSort'}
+
+preconfigopts = "export PSORTROOT=%(installdir)s && "
+
+postinstallcmds = [
+   "cp -r psort/* %(installdir)s/.",
+]
+
+perlmajver = perlver.split('.')[0]
+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
@@ -0,0 +1,130 @@
+# Removed q and a and perl scripting environment set accordingly.
+# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG)
+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 @@
+ </help>
+ <code language="perl">
+ <![CDATA[
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ use Apache::Bio::Tools::PSort;
+ use Bio::Seq;
+ use Data::Dumper;
+diff -ru bio-tools-psort-all/psort/server/startup.pl bio-tools-psort-all.new/psort/server/startup.pl
+--- bio-tools-psort-all/psort/server/startup.pl	2006-08-16 23:41:43.000000000 +0200
++++ bio-tools-psort-all.new/psort/server/startup.pl	2015-11-26 13:51:29.000000000 +0100
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#! /usr/bin/env perl
+
+ use Apache::Bio::Tools::PSort ();
+ use Apache::RPC::Server ();
+diff -ru bio-tools-psort-all/psort/server/www/results.pl bio-tools-psort-all.new/psort/server/www/results.pl
+--- bio-tools-psort-all/psort/server/www/results.pl	2005-03-01 21:38:17.000000000 +0100
++++ bio-tools-psort-all.new/psort/server/www/results.pl	2015-11-26 13:51:41.000000000 +0100
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl -w
++#! /usr/bin/env perl -w
+
+ use Bio::Tools::PSort::Report::Formatter;
+ use Bio::Tools::PSort::XMLRPC::Client;
+diff -ru bio-tools-psort-all/t/sclblast.pl bio-tools-psort-all.new/t/sclblast.pl
+--- bio-tools-psort-all/t/sclblast.pl	2008-10-01 18:57:37.000000000 +0200
++++ bio-tools-psort-all.new/t/sclblast.pl	2015-11-26 13:52:29.000000000 +0100
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+
+ use strict;
+
diff --git a/easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb b/easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb
@@ -0,0 +1,22 @@
+easyblock='ConfigureMake'
+
+name = 'pftoolsV3'
+version = '24.03.16'
+
+homepage = 'http://web.expasy.org/pftools/'
+description = """The pftools package contains all the software necessary to build protein and DNA generalized profiles and use
+ them to scan and align sequences, and search databases.
+"""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+sources = ['%(name)s.tar.gz']
+source_urls = ['ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/%(name)s/']
+checksums = ['ef1d3c7583d764cff06861fca75be455']
+
+sanity_check_paths = {
+    'files': ['bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'