add easyconfigs for SOAPdenovo2, correct location of Ruby easyconfig

easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb

@@ -0,0 +1,31 @@
+#    With <3 for EasyBuild
+#    
+#    EasyConfig for Ruby 2.1:
+#    ----------------------------------------------------------------------------
+#    Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH
+#    License: MIT
+#    Authors: Aaron <aaron.zauner@gmi.oeaw.ac.at> Zauner
+#    ----------------------------------------------------------------------------
+name = 'Ruby'
+version = '2.1.0'
+
+homepage = 'https://www.ruby-lang.org'
+description = """Ruby is a dynamic, open source programming language with 
+ a focus on simplicity and productivity. It has an elegant syntax that is 
+ natural to read and easy to write."""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://cache.ruby-lang.org/pub/ruby/']
+
+sanity_check_paths = {
+    'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb',
+              'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0',
+              'lib/libruby-static.a', 'lib/libruby.so'],
+    'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0']
+}
+
+configopts = "--disable-install-doc --enable-shared"
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-fix-unistd-includes.patch

@@ -0,0 +1,10 @@
+--- SOAPdenovo2-src-r240.orig/sparsePregraph/inc/stdinc.h	2013-07-09 05:46:52.000000000 +0200
++++ SOAPdenovo2-src-r240/sparsePregraph/inc/stdinc.h	2014-04-14 10:07:31.009191162 +0200
+@@ -32,6 +32,7 @@
+ #include <stddef.h>
+ #include <time.h>
+ #include <pthread.h>
++#include <unistd.h>
+ using namespace std;
+
+

easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb

@@ -0,0 +1,38 @@
+#    With <3 for EasyBuild
+#    
+#    EasyConfig for SOAPdenovo2:
+#    ----------------------------------------------------------------------------
+#    Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH
+#    License: MIT
+#    Authors: Petar <petar.forai@gmi.oeaw.ac.at> Forai
+#    ----------------------------------------------------------------------------
+
+easyblock = "MakeCp"
+
+name = 'SOAPdenovo2'
+version = 'r240'
+
+homepage = 'http://soap.genomics.org.cn/index.html'
+description = """SOAPdenovo is a novel short-read assembly method that can build a 
+ de novo draft assembly for human-sized genomes. The program is specially designed to 
+ assemble Illumina short reads. It creates new opportunities for building reference 
+ sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. 
+ SOAPdenovo2 is the successor of SOAPdenovo.""" 
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s-src-%(version)s.tgz']
+
+patches = ['SOAPdenovo2-fix-unistd-includes.patch']
+
+# parallel build is broken
+maxparallel = 1
+
+files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'],
+    'dirs': [],
+}

easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb

@@ -0,0 +1,38 @@
+#    With <3 for EasyBuild
+#    
+#    EasyConfig for SOAPdenovo2:
+#    ----------------------------------------------------------------------------
+#    Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH
+#    License: MIT
+#    Authors: Petar <petar.forai@gmi.oeaw.ac.at> Forai
+#    ----------------------------------------------------------------------------
+
+easyblock = "MakeCp"
+
+name = 'SOAPdenovo2'
+version = 'r240'
+
+homepage = 'http://soap.genomics.org.cn/index.html'
+description = """SOAPdenovo is a novel short-read assembly method that can build a 
+ de novo draft assembly for human-sized genomes. The program is specially designed to 
+ assemble Illumina short reads. It creates new opportunities for building reference 
+ sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. 
+ SOAPdenovo2 is the successor of SOAPdenovo.""" 
+
+toolchain = {'name': 'ictce', 'version': '5.3.0'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s-src-%(version)s.tgz']
+
+patches = ['SOAPdenovo2-fix-unistd-includes.patch']
+
+# parallel build is broken
+maxparallel = 1
+
+files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'],
+    'dirs': [],
+}

easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb

@@ -0,0 +1,38 @@
+#    With <3 for EasyBuild
+#    
+#    EasyConfig for SOAPdenovo2:
+#    ----------------------------------------------------------------------------
+#    Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH
+#    License: MIT
+#    Authors: Petar <petar.forai@gmi.oeaw.ac.at> Forai
+#    ----------------------------------------------------------------------------
+
+easyblock = "MakeCp"
+
+name = 'SOAPdenovo2'
+version = 'r240'
+
+homepage = 'http://soap.genomics.org.cn/index.html'
+description = """SOAPdenovo is a novel short-read assembly method that can build a 
+ de novo draft assembly for human-sized genomes. The program is specially designed to 
+ assemble Illumina short reads. It creates new opportunities for building reference 
+ sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. 
+ SOAPdenovo2 is the successor of SOAPdenovo.""" 
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s-src-%(version)s.tgz']
+
+patches = ['SOAPdenovo2-fix-unistd-includes.patch']
+
+# parallel build is broken
+maxparallel = 1
+
+files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'],
+    'dirs': [],
+}