3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchGotCloud: Alignment Pipeline (view source)
Revision as of 18:16, 19 October 2014
, 18:16, 19 October 2014→Optional Configurable Settings
* BWA_THREADS = -t N
* BWA_THREADS = -t N
** Fill in the N with the number of threads you want BWA to run with, default is 1
** Fill in the N with the number of threads you want BWA to run with, default is 1
* BWA_MAX_MEM = 2000000000
* SORT_MAX_MEM = 2000000000
** Maximum amount of memory used by samtools sort after running bwa
** Maximum amount of memory used by samtools sort after running bwa
*BATCH_TYPE = mosix
*BATCH_TYPE = type
** Tells the cluster gateway to use mosix to send jobs to the client nodes.
** Tells GotCloud to use "type" for sending jobs to the cluster
*BATCH_OPTS = -j36,37,38,39,40,41,45,46,47,48,49
** "type" can be mosix, slurm, slurmi, pbs, sge, sgei
** Specifies which client nodes mosix should send jobs to.
*BATCH_OPTS = options
** replace "options" with the options you want to pass to your cluster type
** For example: BATCH_OPTS = -j36,37,38,39,40,41,45,46,47,48,49
*** Specifies which client nodes mosix should send jobs to.
== Running the Alignment Pipeline ==
== Running the Alignment Pipeline ==
