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Revision as of 09:36, 4 April 2013
, 09:36, 4 April 2013→Running on a Cluster
Here's the same configuration file we used above but now made to run on a cluster computer with MOSIX.
Here's the same configuration file we used above but now made to run on a cluster computer with MOSIX.
== Example Configuration File ==
Example configuration file where reference files happen to be 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
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
OUT_DIR = /path/freeze5/output
OUT_DIR = /path/freeze5/output
REF = /path/reference/hs37d5.fa
REF = /path/reference/hs37d5.fa
INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19
INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19
HM3_VCF = /path/reference/hapmap3_r3_b37.sites.vcf.gz
DBSNP_VCF = /path/reference/dbsnp_135.b37.sites.vcf.gz
BATCH_TYPE = mosix ### Specify MOSIX as the batch system
BATCH_TYPE = mosix ### Specify MOSIX as the batch system
BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes
BATCH_OPTS = -j10,11,12,13 ### Specify available MOSIX compute nodes
