Merge pull request #69 from RoanKanninga/main

new nf_ngs_dna pipeline + new NGS_Automated

g/gVCF2BED/gVCF2BED-1.1.0-GCCcore-11.3.0.eb

@@ -0,0 +1,45 @@
+
+easyblock = 'PackedBinary'
+
+name = 'gVCF2BED'
+version = '1.1.0'
+ngsutilsreleaseversion = '24.02.2'
+
+homepage = 'https://github.com/molgenis/ngs-utils'
+description = """Collection of notes and scripts related to NGS """
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+#
+# Example URL: https://github.com/molgenis/ngs-utils/archive/23.04.1/23.04.1.tar.gz
+#
+source_urls = [('http://github.com/molgenis/ngs-utils/archive/%s/' % (ngsutilsreleaseversion))]
+sources = [('%s.tar.gz' % (ngsutilsreleaseversion))]
+
+checksums = ['294dba4de9ee976fdd863d4997db5f54a933369f6179e7317d8fe99769395b0f']
+
+dependencies = [ 
+    ('gVCF2BEDPyDepBundle','1.0.0' ,'-Python-3.10.4'),
+]
+
+postinstallcmds = [
+    'chmod -R 775 %(installdir)s/bin/*.py',
+]
+
+sanity_check_paths = {
+    'files': ['bin/gvcf2bed2.py', 'bin/group_per_gene.py'],
+    'dirs': []
+}
+
+modextrapaths = {'PATH': 'bin/'}
+
+modloadmsg = """
+===============================================================================
+Show usage:
+       gvcf2bed2.py --help
+
+===============================================================================
+"""
+
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.2.0-AGCT-1.3.0.eb

@@ -0,0 +1,18 @@
+name = 'NGS_Automated'
+version = '4.2.0'
+namelower = name.lower()
+versionsuffix = "-AGCT-1.3.0"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('AGCT', '1.3.0'),
+    ('NGS_Automated', '4.2.0','-bare'),
+    ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0'))
+]
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.2.0-GAP-2.7.0.eb

@@ -0,0 +1,19 @@
+name = 'NGS_Automated'
+version = '4.2.0'
+namelower = name.lower()
+versionsuffix = "-GAP-2.7.0"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('GAP', '2.7.0'),
+    ('NGS_Automated', '4.2.0','-bare'),
+    ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0'))
+]
+
+moduleclass = 'bio'
+

n/NGS_Automated/NGS_Automated-4.2.0-NGS_DNA-4.2.2.eb

@@ -0,0 +1,18 @@
+name = 'NGS_Automated'
+version = '4.2.0'
+namelower = name.lower()
+versionsuffix = "-NGS_DNA-4.2.2"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('NGS_DNA', '4.2.2','',('foss','2022a')),
+    ('NGS_Automated', '4.2.0','-bare'),
+    ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0'))
+]
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.2.0-NGS_Demultiplexing-2.5.3.eb

@@ -0,0 +1,17 @@
+name = 'NGS_Automated'
+version = '4.2.0'
+namelower = name.lower()
+versionsuffix = "-NGS_Demultiplexing-2.5.3"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('NGS_Automated', '4.2.0','-bare'),
+    ('NGS_Demultiplexing', '2.5.3'),
+]
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.2.0-bare.eb

@@ -0,0 +1,29 @@
+name = 'NGS_Automated'
+version = '4.2.0'
+namelower = name.lower()
+versionsuffix='-bare'
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Tarball'
+
+#
+# Example URL: https://github.com/molgenis/NGS_Automated/archive/1.0.1.tar.gz
+# 
+source_urls = [('http://github.com/molgenis/%s/archive/' % (name))]
+sources = [('%s.tar.gz' % (version))]
+
+checksums = ['7baeecaa26e843cad1639f4ad4de81125917d782db39f046360b6f70b0d51712']
+
+sanity_check_paths = {
+    'files': [
+        'bin/moveSequencingData.sh'
+    ],
+    'dirs': [
+        'bin/',
+        'lib',
+    ]
+}
+
+moduleclass = 'bio'

n/NGS_Automated/NGS_Automated-4.2.0-nf_ngs_dna-1.0.0.eb

@@ -0,0 +1,18 @@
+name = 'NGS_Automated'
+version = '4.2.0'
+namelower = name.lower()
+versionsuffix = "-nf_ngs_dna-1.0.0"
+
+homepage = 'https://github.com/molgenis/NGS_Automated'
+description = """Various scripts to automate the NGS pipelines implemented in the MOLGENIS Compute framework."""
+
+toolchain = SYSTEM
+easyblock = 'Bundle'
+
+dependencies = [
+    ('nf_ngs_dna', '1.0.0','',('foss','2022a')),
+    ('NGS_Automated', '4.2.0','-bare'),
+    ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0'))
+]
+
+moduleclass = 'bio'

n/nf_ngs_dna/nf_ngs_dna-1.0.0-foss-2022a.eb

@@ -0,0 +1,35 @@
+easyblock = 'Tarball'
+
+name = 'nf_ngs_dna'
+version = '1.0.0'
+namelower = name.lower()
+
+homepage = 'https://github.com/molgenis/nf_ngs_dna'
+description = """Nexflow ngs_dna pipeline used in the UMCG"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+#
+# Example URL: https://github.com/molgenis/nf_ngs_dna/archive/1.0.0.tar.gz
+#
+source_urls = [('http://github.com/molgenis/%s/archive/' % (name))]
+sources = [('%s.tar.gz' % (version))]
+checksums = ['5aa536249b5dab3788b3bcee279f3124b38f18aae13d1326ca4979731d4ea908']
+
+#
+# Dependencies.
+#
+dependencies = [
+    ('BCFtools', '1.16'),
+    ('BEDTools', '2.30.0'),
+    ('HTSlib', '1.16'),
+    ('ngs-utils', '24.02.2','',('system','')),
+]
+
+
+sanity_check_paths = {
+    'files': ['wgs.nf','swgs.nf'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

n/ngs-utils/ngs-utils-24.02.1.eb

@@ -0,0 +1,31 @@
+name = 'ngs-utils'
+version = '24.02.1'
+
+homepage = 'https://github.com/molgenis/ngs-utils'
+description = """Collection of notes and scripts related to NGS """
+
+toolchain = SYSTEM
+easyblock = 'PackedBinary'
+
+#
+# Example URL: https://github.com/molgenis/ngs-utils/archive/23.02.1.tar.gz
+#
+source_urls = [('http://github.com/molgenis/ngs-utils/archive/%s/' % (version))]
+sources = [('%s.tar.gz' % (version))]
+
+checksums = ['950b3fc8c5622c2fa6d2831d8474acd227f70ae6ee680bc5cc6a413a295a0943']
+
+postinstallcmds = [
+    'chmod -R 775 %(installdir)s/bin/*.sh',
+    'chmod -R 775 %(installdir)s/bin/*.bash',
+    'chmod -R 775 %(installdir)s/bin/*.pl',
+    'chmod -R 775 %(installdir)s/bin/*.py',
+    'chmod -R g+rwX,o+rX,o-w %(installdir)s/bin/*'
+]
+
+sanity_check_paths = {
+    'files': ['bin/compareWithVKGL_gatk4_b38.sh'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

n/ngs-utils/ngs-utils-24.02.2.eb

@@ -0,0 +1,31 @@
+name = 'ngs-utils'
+version = '24.02.2'
+
+homepage = 'https://github.com/molgenis/ngs-utils'
+description = """Collection of notes and scripts related to NGS """
+
+toolchain = SYSTEM
+easyblock = 'PackedBinary'
+
+#
+# Example URL: https://github.com/molgenis/ngs-utils/archive/23.02.1.tar.gz
+#
+source_urls = [('http://github.com/molgenis/ngs-utils/archive/%s/' % (version))]
+sources = [('%s.tar.gz' % (version))]
+
+checksums = ['294dba4de9ee976fdd863d4997db5f54a933369f6179e7317d8fe99769395b0f']
+
+postinstallcmds = [
+    'chmod -R 775 %(installdir)s/bin/*.sh',
+    'chmod -R 775 %(installdir)s/bin/*.bash',
+    'chmod -R 775 %(installdir)s/bin/*.pl',
+    'chmod -R 775 %(installdir)s/bin/*.py',
+    'chmod -R g+rwX,o+rX,o-w %(installdir)s/bin/*'
+]
+
+sanity_check_paths = {
+    'files': ['bin/compareWithVKGL_gatk4_b38.sh'],
+    'dirs': []
+}
+
+moduleclass = 'bio'