Merge pull request #44 from fgeorgatos/contrib_bio_moduleclasses

boegel · boegel · commit 1df62dd0e08c · 2012-12-05T05:11:08.000-08:00
redefined bioinformatics packages in the "bio" moduleclass and cleanup leftover buildstats
diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb
@@ -30,3 +30,5 @@ sanity_check_paths = {
                      }
 
 parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb
@@ -30,3 +30,5 @@ sanity_check_paths = {
                      }
 
 parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/BWA/BWA-0.6.2-goalf-1.1.0-no-OFED.eb
@@ -19,3 +19,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 
 sources = ['%s-%s.tar.bz2' % (name.lower(), version)]
 source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/b/BWA/BWA-0.6.2-ictce-4.0.6.eb
@@ -19,3 +19,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 
 sources = ['%s-%s.tar.bz2' % (name.lower(), version)]
 source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/BiSearch/BiSearch-20051222-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/BiSearch/BiSearch-20051222-goalf-1.1.0-no-OFED.eb
@@ -7,3 +7,5 @@ description = """BiSearch is a primer-design algorithm for DNA sequences."""
 toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'}
 
 sources = ['%s_%s.tar.gz' % (name.lower(), version)]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/BiSearch/BiSearch-20051222-ictce-4.0.6.eb b/easybuild/easyconfigs/b/BiSearch/BiSearch-20051222-ictce-4.0.6.eb
@@ -7,3 +7,5 @@ description = """BiSearch is a primer-design algorithm for DNA sequences."""
 toolchain = {'name': 'ictce', 'version': '4.0.6'}
 
 sources = ['%s_%s.tar.gz' % (name.lower(), version)]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.0-beta7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.0-beta7-goalf-1.1.0-no-OFED.eb
@@ -20,3 +20,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 sources = ['%s-%s-source.zip' % (name.lower(), version)]
 source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')]
 # N.B. the download option above -> required for sourceforge
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.0-beta7-ictce-4.0.6.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.0-beta7-ictce-4.0.6.eb
@@ -20,3 +20,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 sources = ['%s-%s-source.zip' % (name.lower(), version)]
 source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')]
 # N.B. the download option above -> required for sourceforge
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb
@@ -25,15 +25,4 @@ sanity_check_paths = {
                       'dirs': []
                      }
 
-#Build statistics
-buildstats=[
-                 {
-                  'timestamp': 1346797039,
-                  'cpu_model': 'Intel(R) Xeon(R) CPU           L5640  @ 2.27GHz',
-                  'build_time': 53.079999999999998,
-                  'platform': 'Linux-2.6.32-5-amd64-x86_64-with-debian-6.0.5',
-                  'host': 'gaia-11',
-                  'install_size': 845303,
-                  'core_count': 12
-                 }
-           ]
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb
@@ -25,15 +25,4 @@ sanity_check_paths = {
                       'dirs': []
                      }
 
-#Build statistics
-buildstats=[
-                 {
-                  'timestamp': 1346797039,
-                  'cpu_model': 'Intel(R) Xeon(R) CPU           L5640  @ 2.27GHz',
-                  'build_time': 53.079999999999998,
-                  'platform': 'Linux-2.6.32-5-amd64-x86_64-with-debian-6.0.5',
-                  'host': 'gaia-11',
-                  'install_size': 845303,
-                  'core_count': 12
-                 }
-           ]
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb
@@ -36,3 +36,5 @@ sanity_check_paths = {
                                                              'masker']],
                       'dirs': ['.']
                      }
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb
@@ -38,3 +38,5 @@ sanity_check_paths = {
                                                              'masker']],
                       'dirs': ['.']
                      }
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb
@@ -18,3 +18,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 
 sources = ['%s%s.tar.gz'%(name, version)]
 source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb
@@ -18,3 +18,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 
 sources = ['%s%s.tar.gz'%(name, version)]
 source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb
@@ -24,3 +24,5 @@ source_urls = ['http://metavelvet.dna.bio.keio.ac.jp/src']
 dependencies = [('Velvet', '1.2.07')]
 
 parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb
@@ -24,3 +24,5 @@ source_urls = ['http://metavelvet.dna.bio.keio.ac.jp/src']
 dependencies = [('Velvet', '1.2.07')]
 
 parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goalf-1.1.0-no-OFED.eb
@@ -10,3 +10,4 @@ toolchainopts={'optarch':True, 'usempi':True}
 sources=['%s-%s.tar.gz'%(name.lower(),version)]
 source_urls=["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)]
 
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-4.0.6.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-4.0.6.eb
@@ -10,3 +10,4 @@ toolchainopts={'optarch':True, 'usempi':True}
 sources=['%s-%s.tar.gz'%(name.lower(),version)]
 source_urls=["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)]
 
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goalf-1.1.0-no-OFED.eb
@@ -11,3 +11,5 @@ sources=['%s-%s.tar.gz'%(name.lower(),version)]
 source_urls=["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)]
 
 dependencies=[('BEAGLE','20120124')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-4.0.6.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-4.0.6.eb
@@ -11,3 +11,5 @@ sources=['%s-%s.tar.gz'%(name.lower(),version)]
 source_urls=["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)]
 
 dependencies=[('BEAGLE','20120124')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-goalf-1.1.0-no-OFED.eb
@@ -16,3 +16,5 @@ patches = ['old-libstdc++-hash_fun-map-set.patch']
 
 # Pasha's makefile is not suited for parallel execution 
 parallel = 1
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.3-ictce-4.0.6.eb
@@ -20,3 +20,5 @@ patches = [
 
 # Pasha's makefile is not suited for parallel execution 
 parallel = 1
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-4.0.6.eb
@@ -22,3 +22,5 @@ patches = [
 
 # Pasha's makefile is not suited for parallel execution 
 parallel = 1
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb
@@ -24,3 +24,5 @@ sanity_check_paths = {
                       'files': ['bin/RNAz'],
                       'dirs': []
                      }
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-4.0.6.eb
@@ -24,3 +24,5 @@ sanity_check_paths = {
                       'files': ['bin/RNAz'],
                       'dirs': []
                      }
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goalf-1.1.0-no-OFED.eb
@@ -22,3 +22,5 @@ source_urls = [('http://sourceforge.net/projects/samtools/files/%s/%s' % (name.l
 patches = ['SAMtools_Makefile-ncurses.patch']
 
 dependencies = [('ncurses', '5.9')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-4.0.6.eb
@@ -22,3 +22,5 @@ source_urls = [('http://sourceforge.net/projects/samtools/files/%s/%s' % (name.l
 patches = ['SAMtools_Makefile-ncurses.patch']
 
 dependencies = [('ncurses', '5.9')]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SHRiMP/SHRiMP-2.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SHRiMP/SHRiMP-2.2.3-goalf-1.1.0-no-OFED.eb
@@ -11,3 +11,4 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'}
 source_urls = ['http://compbio.cs.toronto.edu/shrimp/releases']
 sources = ['%s_%s.src.tar.gz' % (name, '_'.join(version.split('.')))]
 
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SHRiMP/SHRiMP-2.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SHRiMP/SHRiMP-2.2.3-ictce-4.0.6.eb
@@ -11,3 +11,4 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'}
 source_urls = ['http://compbio.cs.toronto.edu/shrimp/releases']
 sources = ['%s_%s.src.tar.gz' % (name, '_'.join(version.split('.')))]
 
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-goalf-1.1.0-no-OFED.eb
@@ -20,3 +20,4 @@ toolchainopts = {'optarch': True, 'pic': True}
 sources = ['%s-V%s.src.tgz' % (name, version)]
 source_urls = ['http://soap.genomics.org.cn/down']
 
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-ictce-4.0.6.eb
@@ -20,3 +20,4 @@ toolchainopts = {'optarch': True, 'pic': True}
 sources = ['%s-V%s.src.tgz' % (name, version)]
 source_urls = ['http://soap.genomics.org.cn/down']
 
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb
@@ -18,3 +18,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 
 sources = ['%s_%s.tgz' % (name.lower(), version)]
 source_urls = ['http://www.ebi.ac.uk/~zerbino/%s' % name.lower()]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-ictce-4.0.6.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-ictce-4.0.6.eb
@@ -18,3 +18,5 @@ toolchainopts = {'optarch': True, 'pic': True}
 
 sources = ['%s_%s.tgz' % (name.lower(), version)]
 source_urls = ['http://www.ebi.ac.uk/~zerbino/%s' % name.lower()]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb
@@ -36,3 +36,4 @@ sanity_check_paths = {
                       'dirs': []
                      }
 
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb
@@ -38,3 +38,4 @@ sanity_check_paths = {
                       'dirs': []
                      }
 
+moduleclass = 'bio'

Original file line number	Diff line number	Diff line change
`@@ -30,3 +30,5 @@ sanity_check_paths = {`
`30`	`30`	`}`
`31`	`31`
`32`	`32`	`parallel = 1 # make crashes otherwise`
	`33`	`+`
	`34`	`+moduleclass = 'bio'`