diff --git a/c/ConcordanceCheck/ConcordanceCheck-2.2.0.eb b/c/ConcordanceCheck/ConcordanceCheck-2.2.0.eb new file mode 100644 index 0000000..75cd0c9 --- /dev/null +++ b/c/ConcordanceCheck/ConcordanceCheck-2.2.0.eb @@ -0,0 +1,36 @@ +name = 'ConcordanceCheck' +version = '2.2.0' +namelower = name.lower() +homepage = 'https://github.com/molgenis/ConcordanceCheck' +description = """Various scripts to automate and execute the ConcordanceCheck implemented in the MOLGENIS Compute framework.""" + +toolchain = SYSTEM +easyblock = 'Tarball' + +# +# Example URL: https://github.com/molgenis/ConcordanceCheck/archive/2.2.0.tar.gz +# +source_urls = [('http://github.com/molgenis/%s/archive/' % (name))] +sources = [('%s.tar.gz' % (version))] + +checksums = ['985020a96b37f9adfd68beb7a352799aa22aaa74b4f812759258d7729f9fd1c0'] + +dependencies = [ + ('CompareGenotypeCalls', '1.8.1', '-Java-8-LTS'), +] + +sanity_check_paths = { + 'files': [ + 'bin/ConcordanceCheck.sh', + 'bin/ParseDarwinSamplesheet.sh', + 'bin/copyConcordanceCheckData.sh', + 'bin/notifications.sh', + 'etc/sharedConfig.cfg', + 'lib/sharedFunctions.bash', + ], + 'dirs': [ + 'etc/cron.d', + ] +} + +moduleclass = 'bio' diff --git a/g/gVCF2BED/gVCF2BED-1.0.0-GCCcore-11.3.0.eb b/g/gVCF2BED/gVCF2BED-1.0.0-GCCcore-11.3.0.eb index aa44c9b..351b2b8 100644 --- a/g/gVCF2BED/gVCF2BED-1.0.0-GCCcore-11.3.0.eb +++ b/g/gVCF2BED/gVCF2BED-1.0.0-GCCcore-11.3.0.eb @@ -11,7 +11,7 @@ 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/refs/tags/23.04.1.tar.gz +# 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))] diff --git a/n/NGS_Automated/NGS_Automated-4.0.0-AGCT-1.3.0.eb b/n/NGS_Automated/NGS_Automated-4.0.0-AGCT-1.3.0.eb new file mode 100644 index 0000000..c81e544 --- /dev/null +++ b/n/NGS_Automated/NGS_Automated-4.0.0-AGCT-1.3.0.eb @@ -0,0 +1,18 @@ +name = 'NGS_Automated' +version = '4.0.0' +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', '4.0.0','-bare'), + ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0')) +] + +moduleclass = 'bio' diff --git a/n/NGS_Automated/NGS_Automated-4.0.0-GAP-2.7.0.eb b/n/NGS_Automated/NGS_Automated-4.0.0-GAP-2.7.0.eb new file mode 100644 index 0000000..d9d68f8 --- /dev/null +++ b/n/NGS_Automated/NGS_Automated-4.0.0-GAP-2.7.0.eb @@ -0,0 +1,19 @@ +name = 'NGS_Automated' +version = '4.0.0' +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', '4.0.0','-bare'), + ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0')) +] + +moduleclass = 'bio' + diff --git a/n/NGS_Automated/NGS_Automated-4.0.0-NGS_DNA-4.2.1.eb b/n/NGS_Automated/NGS_Automated-4.0.0-NGS_DNA-4.2.1.eb new file mode 100644 index 0000000..3fab26d --- /dev/null +++ b/n/NGS_Automated/NGS_Automated-4.0.0-NGS_DNA-4.2.1.eb @@ -0,0 +1,18 @@ +name = 'NGS_Automated' +version = '4.0.0' +namelower = name.lower() +versionsuffix = "-NGS_DNA-4.2.1" + +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', '4.2.1','',('foss','2022a')), + ('NGS_Automated', '4.0.0','-bare'), + ('hashdeep', '4.4-20180907-18a6b5d','', ('GCCcore','11.3.0')) +] + +moduleclass = 'bio' diff --git a/n/NGS_Automated/NGS_Automated-4.0.0-NGS_Demultiplexing-2.5.3.eb b/n/NGS_Automated/NGS_Automated-4.0.0-NGS_Demultiplexing-2.5.3.eb new file mode 100644 index 0000000..e701c55 --- /dev/null +++ b/n/NGS_Automated/NGS_Automated-4.0.0-NGS_Demultiplexing-2.5.3.eb @@ -0,0 +1,17 @@ +name = 'NGS_Automated' +version = '4.0.0' +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', '4.0.0','-bare'), + ('NGS_Demultiplexing', '2.5.3'), +] + +moduleclass = 'bio' diff --git a/n/NGS_Automated/NGS_Automated-4.0.0-bare.eb b/n/NGS_Automated/NGS_Automated-4.0.0-bare.eb new file mode 100644 index 0000000..67ff9ab --- /dev/null +++ b/n/NGS_Automated/NGS_Automated-4.0.0-bare.eb @@ -0,0 +1,31 @@ +name = 'NGS_Automated' +version = '4.0.0' +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 = ['9bb7b1bfb71d10f71323e3ad7afa3b3ad48cf8f9e8dbc91502acd0e4cf70b52a'] + +sanity_check_paths = { + 'files': [ + 'bin/PullAndProcessGsAnalysisData.sh', + 'etc/betabarrel.cfg', + ], + 'dirs': [ + 'bin/', + 'etc/cron.d', + 'lib', + ] +} + +moduleclass = 'bio' diff --git a/n/NGS_DNA/NGS_DNA-4.2.1-foss-2022a.eb b/n/NGS_DNA/NGS_DNA-4.2.1-foss-2022a.eb new file mode 100644 index 0000000..ffa0c81 --- /dev/null +++ b/n/NGS_DNA/NGS_DNA-4.2.1-foss-2022a.eb @@ -0,0 +1,60 @@ +easyblock = 'Tarball' + +name = 'NGS_DNA' +version = '4.2.1' +namelower = name.lower() + +homepage = 'https://github.com/molgenis/NGS_DNA' +description = """NGS_DNA pipeline used in the UMCG""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +javaver = '8-LTS' +py3ver = '3.10.4' +py2ver = '2.7.16' + +# +# Example URL: https://github.com/molgenis/NGS_DNA/archive/3.2.3.tar.gz +# +source_urls = [('http://github.com/molgenis/%s/archive/' % (name))] +sources = [('%s.tar.gz' % (version))] +checksums = ['a6f7c62f22d84ada86deb5a12e2f79ac5fe44607575842da4375466fa74bfc14'] + +# +# Dependencies. +# +dependencies = [ +# ('VCFped','20180527_d1bbdf5','-Python-%s' % (py2ver),('foss','2018b')), +# ('manta','1.6.0'), +# ('CADD', 'v1.4','',('foss','2018b')), + ('BCFtools', '1.16'), + ('BEDTools', '2.30.0'), + ('BWA', '0.7.17-20220923-139f68f'), + ('FastQC', '0.11.9', '-Java-%s' % (javaver), ('system', '')), + ('GATK', '4.2.4.1', '-Java-8-LTS', ('system', '')), + ('gVCF2BED','1.0.0'), + ('jq','1.6'), + ('HTSlib', '1.16'), + ('ngs-utils', '22.10.1','',('system','')), + ('pigz', '2.7',''), + ('picard', '2.26.10', '-Java-%s' % (javaver), ('system', '')), + ('gavin-plus', '1.5.0', '-Java-%s' % (javaver), ('system', '')), + ('io_lib', '1.14.11'), + ('Molgenis-Compute', '20.03.1', '-Java-11-LTS', ('system', '')), + ('multiqc', '1.12'), + ('R','4.2.1','-bare'), + ('sambamba', '0.7.0', '', ('system', '')), + ('SAMtools', '1.16.1'), + ('seqtk', '1.3'), + ('snpEff', '4.3t', '-Java-%s' % (javaver), ('system', '')), + ('vcfanno', 'v0.3.3', '', ('system', '')), +] + + +sanity_check_paths = { + 'files': ['workflow_DRAGEN.csv', 'parameters.csv'], + 'dirs': [] +} + +moduleclass = 'bio' +modextrapaths = {'PATH': ['scripts/']} diff --git a/n/NGS_Demultiplexing/NGS_Demultiplexing-2.5.3.eb b/n/NGS_Demultiplexing/NGS_Demultiplexing-2.5.3.eb index 9fe9802..62bf043 100644 --- a/n/NGS_Demultiplexing/NGS_Demultiplexing-2.5.3.eb +++ b/n/NGS_Demultiplexing/NGS_Demultiplexing-2.5.3.eb @@ -5,7 +5,7 @@ namelower = name.lower() homepage = 'https://github.com/molgenis/molgenis-pipelines' description = """This distribution already contains several pipelines/protocols/parameter files which you can use 'out-of-the-box' to align and impute your NGS data using MOLGENIS Compute.""" -toolchain = {'name': 'system', 'version': ''} +toolchain = SYSTEM easyblock = 'Tarball' #dependencies