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## ----------------------- f l o w r config ------------------------ ##
## the file by default, sits in the R pacakge
## You may copy this to ~/flowr/conf
## --------------------------------------------------------------------- ##
## Following lines, as a tab delimited table, with two columns
## Add flow_ to each name, to make them easily identifiable.
## Always use load_conf(); after editing this file !
verbose 1 ## this operates on levels. 0: absolutely silent. 1: recommended. 2: debug
flow_base_path ~/flowr ## flowr home, dont change !
flow_conf_path {{flow_base_path}}/conf ## custom configuration files sit, dont change !
flow_run_path ~/flowr/runs ## home of all executed flows, you may change this
flow_pipe_paths ~/flowr/pipelines
flow_pipe_urls ~/flowr/pipelines
## --- some configurations regarding the platform, not used extensively at the moment
flow_platform local ## default platform. Options: lsf, moab, torque, local, sge
# version >= 0.9.8.9004
local_cores 4 ## max number of cores to use when running on a local server
## --- parsing jobs IDs
## regular expressions which will parse and provide the jobids
flow_parse_torque "(.?)\\..*" ## example: 40947.dqsfacpriv01.mdanderson.edu
flow_parse_lsf ".*(\\<[0-9]*\\>).*" ##
flow_parse_moab (.*) ##
flow_parse_sge (.*) ##
flow_parse_slurm ".* ([0-9]+)" ## example: Submitted batch job 1234
# default module of a pipeline
# version >= 0.9.8.9015
module_cmds ''
## examples: one may define all modules used in a pipeline here,
## further one may specify any other command which should be run before
## script executes
#module_cmds 'module load samtools;PATH=$PATH:/apps/bin'
# time format to be used in scripts, in BGN and END statements
time_format "%a %b %e %H:%M:%S CDT %Y"