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Psortb foss2016a #3317
Psortb foss2016a #3317
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Original file line number | Diff line number | Diff line change |
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@@ -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 | ||
## | ||
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easyblock = 'ConfigureMake' | ||
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name = 'BLAST+' | ||
version = '2.3.0' | ||
versionsuffix = '-Python-2.7.11' | ||
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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.""" | ||
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toolchain = {'name': 'foss', 'version': '2016a'} | ||
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sources = ['ncbi-blast-%(version)s+-src.tar.gz'] | ||
source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] | ||
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dependencies = [('Boost', '1.58.0', versionsuffix)] | ||
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configopts = '--with-boost=$EBROOTBOOST --with-64' | ||
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sanity_check_paths = { | ||
'files': ["bin/blastn", "bin/blastp", "bin/blastx"], | ||
'dirs': [] | ||
} | ||
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moduleclass = 'bio' |
Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,43 @@ | ||
easyblock = 'PerlModule' | ||
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name = 'PSORTb' | ||
version = '3.0.4' | ||
versionsuffix = '-Perl-%(perlver)s' | ||
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homepage = 'http://psort.org/psortb/index.html' | ||
description = """PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.""" | ||
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toolchain = {'name': 'foss', 'version': '2016a'} | ||
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source_urls = ['http://www.psort.org/download/'] | ||
sources = ['bio-tools-psort-all.%(version)s.tar.gz'] | ||
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patches = [ | ||
'PSORTb-%(version)s-libpsortb.patch', | ||
'PSORTb-%(version)s_CC.patch', | ||
] | ||
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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'), | ||
] | ||
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options = {'modulename': 'Bio::Tools::PSort'} | ||
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preconfigopts = "export PSORTROOT=%(installdir)s && " | ||
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postinstallcmds = [ | ||
"cp -r psort/* %(installdir)s/.", | ||
] | ||
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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'], | ||
} | ||
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moduleclass = 'bio' |
Original file line number | Diff line number | Diff line change |
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@@ -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 @@ | ||
} | ||
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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; | ||
} | ||
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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 | ||
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use Getopt::Long; | ||
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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 | ||
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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 | ||
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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 | ||
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use Getopt::Long; | ||
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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 | ||
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use Getopt::Long; | ||
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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 | ||
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use Getopt::Long; | ||
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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 | ||
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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 | ||
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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 | ||
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use strict; | ||
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@@ -0,0 +1,13 @@ | ||
#Subtitue hardcoded cc for gcc to prevent 'cc1: error: unrecognized command line option "-fstack-protector-strong"' | ||
#Author: Ruben van Dijk (University of Groningen) | ||
--- bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:30.000000000 +0200 | ||
+++ bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:14.000000000 +0200 | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. @RvDijk the patch doesn't work because the Two options:
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@@ -34,7 +34,7 @@ | ||
# These definitions are from config.sh (via /software/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/Config.pm). | ||
# They may have been overridden via Makefile.PL or on the command line. | ||
AR = ar | ||
-CC = cc | ||
+CC = gcc | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. @RvDijk it's better/safer to use this construct, which should result in inheriting the
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CCCDLFLAGS = -fPIC | ||
CCDLFLAGS = -Wl,-E | ||
DLEXT = so |
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@@ -0,0 +1,22 @@ | ||
easyblock='ConfigureMake' | ||
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name = 'pftoolsV3' | ||
version = '20160324' | ||
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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. | ||
""" | ||
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toolchain = {'name': 'foss', 'version': '2016a'} | ||
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sources = ['%(name)s.tar.gz'] | ||
source_urls = ['ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/%(name)s/'] | ||
checksums = ['ef1d3c7583d764cff06861fca75be455'] | ||
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sanity_check_paths = { | ||
'files': ['bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch'], | ||
'dirs': [], | ||
} | ||
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moduleclass = 'bio' |
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please include a comment in the patch explaining what it does, and who the author is