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837 bytes added
, 09:21, 2 April 2013
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| == Example Configuration File == | | == Example Configuration File == |
− | Example Configuration file where reference files are stored in /path/reference, and bam index file in path/freeze5 | + | Example configuration file where reference files are stored in /path/reference, and bam index file in path/freeze5 |
| + | CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| + | BAM_INDEX = /path/freeze5/freeze5.bam.index ### The BAM index file described above |
| + | OUT_DIR = /path/freeze5/output ### Directory in which to put all gotcloud output |
| + | REF = /path/reference/hs37d5.fa ### Reference sequence |
| + | INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19 ### Known indel sites |
| + | HM3_PREFIX = /path/reference/hapmap3_r3_b37_fwd.consensus.qc.poly ### HapMap variants |
| + | DBSNP_PREFIX = /path/reference/dbsnp_129_b37.rod ### dbSNP variants |
| + | |
| + | Here's the same configuration file but made to run on a cluster computer with MOSIX. |
| CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | | CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| BAM_INDEX = /path/freeze5/freeze5.bam.index | | BAM_INDEX = /path/freeze5/freeze5.bam.index |
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| HM3_PREFIX = /path/reference/hapmap3_r3_b37_fwd.consensus.qc.poly | | HM3_PREFIX = /path/reference/hapmap3_r3_b37_fwd.consensus.qc.poly |
| DBSNP_PREFIX = /path/reference/dbsnp_129_b37.rod | | DBSNP_PREFIX = /path/reference/dbsnp_129_b37.rod |
| + | BATCH_TYPE = mosix ### Specify MOSIX as the batch system |
| + | BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes |
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| = Running = | | = Running = |