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Revision as of 09:28, 2 April 2013
, 09:28, 2 April 2013→Running on a Cluster
To run on the Cluster, the following settings need to be added to the configuration file:
To run on the Cluster, the following settings need to be added to the configuration file:
<--- Following may need revision --->
TODO: COMING SOON
TODO: COMING SOON
SLEEP_MULT = 20
SLEEP_MULT = 20
REMOTE_PREFIX = # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir])
REMOTE_PREFIX = # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir])
<--- End: Following may need revision --->
Here's the same configuration file we used above 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
BAM_INDEX = /path/freeze5/freeze5.bam.index
OUT_DIR = /path/freeze5/output
REF = /path/reference/hs37d5.fa
INDEL_PREFIX = /path/reference/1kg.pilot_release.merged.indels.sites.hg19
HM3_PREFIX = /path/reference/hapmap3_r3_b37_fwd.consensus.qc.poly
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
= Results =
= Results =
