| 1 | name = 'GATK' |
|---|
| 2 | version = '3.3-0' |
|---|
| 3 | |
|---|
| 4 | homepage = 'http://www.broadinstitute.org/gatk/' |
|---|
| 5 | description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute |
|---|
| 6 | to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, |
|---|
| 7 | with a primary focus on variant discovery and genotyping as well as strong emphasis on |
|---|
| 8 | data quality assurance. Its robust architecture, powerful processing engine and |
|---|
| 9 | high-performance computing features make it capable of taking on projects of any size.""" |
|---|
| 10 | |
|---|
| 11 | toolchain = {'name': 'dummy', 'version': 'dummy'} |
|---|
| 12 | easyblock = 'Tarball' |
|---|
| 13 | |
|---|
| 14 | # download manually from http://www.broadinstitute.org/gatk/download |
|---|
| 15 | sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] |
|---|
| 16 | |
|---|
| 17 | java = 'Java' |
|---|
| 18 | javaver = '1.7.0_76' |
|---|
| 19 | versionsuffix = '-%s-%s' % (java, javaver) |
|---|
| 20 | dependencies = [(java, javaver)] |
|---|
| 21 | |
|---|
| 22 | modloadmsg = """To execute GATK run: java -jar \\${EBROOTGATK}/GenomeAnalysisTK.jar""" |
|---|
| 23 | |
|---|
| 24 | sanity_check_paths = { |
|---|
| 25 | 'files': ["GenomeAnalysisTK.jar"], |
|---|
| 26 | 'dirs': ["resources"], |
|---|
| 27 | } |
|---|
| 28 | |
|---|
| 29 | moduleclass = 'bio' |
|---|
