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Psortb foss2016a #3317
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Psortb foss2016a #3317
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a9d2a80
psortb with foss2016a
RvDijk f43ff29
BLAST+ in BLAST+ folder
RvDijk a0b242a
include patch
RvDijk 6d1ac74
include patch
RvDijk 2746609
pftools rename, perlversion used properly
RvDijk 055e276
version change, removed perlmajver
RvDijk c3e97c9
version change for pftoolsV3 dep
RvDijk 75aa60a
format of date
RvDijk 75f0cd7
use BLAST instead of BLAST+
RvDijk a4ce580
use BLAST instead of BLAST+
RvDijk dc39cdf
provide patch for hardcoded CC
RvDijk 113096c
update patch file
RvDijk 26042f4
Update patch to inherit value from env
RvDijk 2cb8101
use sed to remove hardcoded CC in makefile
RvDijk 64c793b
Use sed for hardcoded CC and removed patch
RvDijk File filter
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38 changes: 38 additions & 0 deletions
38
easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb
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## | ||
# 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' |
43 changes: 43 additions & 0 deletions
43
easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb
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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' |
130 changes: 130 additions & 0 deletions
130
easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch
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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 | ||
CCCDLFLAGS = -fPIC | ||
CCDLFLAGS = -Wl,-E | ||
DLEXT = so |
22 changes: 22 additions & 0 deletions
22
easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb
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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