Updated BBMap

Updated bcl-convert
Updated cbc_pacbio
Updated cbc_scripts

easyconfigs/b/BBMap/BBMap-39.06-Java-15.0.1.eb

@@ -0,0 +1,35 @@
+easyblock = 'MakeCp'
+
+name = 'BBMap'
+version = '39.06'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://sourceforge.net/projects/bbmap/'
+description = """BBMap short read aligner, and other bioinformatic tools."""
+
+toolchain = SYSTEM
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s_%(version)s.tar.gz']
+
+dependencies = [('Java', '15.0.1', '', True)]
+
+prebuildopts = 'cd jni && '
+
+local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
+buildopts = "-f makefile.%s" % local_suff
+
+files_to_copy = ['*']
+
+sanity_check_paths = {
+ 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT],
+ 'dirs': []
+}
+
+modextrapaths = {'PATH': ''}
+
+modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the"
+modloadmsg += " compiled jni C code.\n"
+
+moduleclass = 'bio'
+

easyconfigs/b/bcl-convert/bcl-convert-4.2.4.eb

@@ -0,0 +1,26 @@
+easyblock = 'Rpm'
+
+name = 'bcl-convert'
+version = '4.2.4'
+
+homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html?langsel=/us/'
+description = """The Illumina BCL Convert"""
+
+toolchain = SYSTEM
+
+sources = ['bcl-convert-%(version)s-2.el7.x86_64.rpm']
+source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/']
+
+dependencies = [
+]
+
+keepsymlinks = True
+
+sanity_check_paths = {
+ 'files': ['usr/bin/bcl-convert'],
+ 'dirs': [],
+}
+
+modextrapaths = {}
+
+moduleclass = 'bio'

easyconfigs/c/cbc_pacbio/cbc_pacbio-3.2-IGB-gcc-8.2.0.eb

@@ -0,0 +1,46 @@
+easyblock = 'Tarball'
+
+name = 'cbc_pacbio'
+version = '3.2'
+
+homepage = 'https:/IGBIllinois/cbc_pacbio'
+description = """Command-line scripts and pipelines to perform downstream analyses of Sequel II subreads"""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+
+sources = [{
+ 'filename': 'cbc_pacbio-%(version)s.tar.gz',
+ 'git_config': {
+ 'url': 'https:/IGBIllinois',
+ 'repo_name': 'cbc_pacbio',
+ 'tag': '%(version)s',
+ },
+}]
+
+dependencies = [('Perl','5.28.1'),
+ ('tar','1.32'),
+ ('pigz','2.4'),
+ ('pbzip2','1.1.13'),
+ ('MultiQC','1.7','-Python-3.7.2'),
+ ('FastQC','0.11.7','-Java-1.8.0_201',True),
+ ('seqtk','1.2'),
+ ('SAMtools','1.10'),
+ ('gnuplot','4.6.7'),
+ ('smrtlink','11.1.0.166339','',True),
+ ('pbbam','1.0.7'),
+ ('seqkit','0.15.0','',True),
+]
+
+keepsymlinks = True
+
+sanity_check_paths = {
+ 'files': ['bin/hifi_demult_standalone.sh'],
+ 'dirs': [],
+}
+
+postinstallcmds = ['chmod 775 %(installdir)s/bin/*']
+
+modextrapaths = {}
+
+moduleclass = 'bio'

easyconfigs/c/cbc_scripts/cbc_scripts-1.25-IGB-gcc-8.2.0.eb

@@ -0,0 +1,48 @@
+easyblock = 'Tarball'
+
+name = 'cbc_scripts'
+version = '1.25'
+
+homepage = 'https:/IGBIllinois/CBC_scripts'
+description = """DNA services at the Biotech center include short read sequencing with four types of Illumina platforms: HiSeq4000, HiSeq2500, MiSeq and NovaSeq6000"""
+
+toolchain = {'name': 'IGB-gcc', 'version': '8.2.0'}
+
+sources = [{
+ 'filename': 'cbc_scripts-%(version)s.tar.gz',
+ 'git_config': {
+ 'url': 'https:/IGBIllinois',
+ 'repo_name': 'CBC_scripts',
+ 'tag': '%(version)s',
+ },
+}]
+
+dependencies = [
+ ('Perl','5.28.1'),
+ ('bcl2fastq2','2.20'),
+ ('pigz','2.4'),
+ ('pbzip2','1.1.13'),
+ ('BLAST+','2.13.0'),
+ ('FASTX-Toolkit','0.0.13.2','',True),
+ ('MultiQC','1.12','-Python-3.7.2'),
+ ('FastQC','0.11.9','-Java-15.0.1',True),
+ ('SQLite','3.17.0'),
+ ('seqtk','1.2'),
+ ('gnuplot','4.6.7'),
+ ('Bowtie2','2.4.5'),
+ ('fastp','0.20.1'),
+ ('PrimerMgr','1.05','-Java-15.0.1',True),
+ ('seqkit','2.3.0','',True),
+]
+
+configopts = ''
+sanity_check_paths = {
+ 'files': ['bin/fluidigmPrimerSort.pl'],
+ 'dirs': [],
+}
+
+modextrapaths = {}
+
+moduleclass = 'bio'
+
+