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Revision as of 09:21, 2 April 2013
, 09:21, 2 April 2013→Example Configuration File
== 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
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
= Running =
= Running =
