vadr.qsubinfo

# vadr.qsubinfo
# This file must have exactly 2 non-'#' prefixed
# lines. 
#
# Line 1: a string that is the qsub command and flags for submitting
# jobs to the compute farm *prior* to the actual cmsearch/cmalign command.
#
# This line may have up to four special values that will be
# replaced: 
# (a) "![errfile]!": will be replaced by an error file name
#     automatically determined by VADR
# (b) "![jobname]!": will be replaced by a job name
#     automatically determined by VADR
# (c) "![memgb]!": will be replaced by number of Gb of required memory
#     automatically determined by VADR
#     changeable via the --mxsize option to v-annotate.pl    
# (d) "![nsecs]!": will be replaced by number of seconds of run time
#     to allow for the job, automatically determined by VADR,
#     changeable via the --wait option to v-annotate.pl    
#
# Line 2: the remainder of the qsub cmsearch/cmalign command 
#
qsub -N ![jobname]! -b y -v SGE_FACILITIES -P unified -S /bin/bash -cwd -V -j n -o /dev/null -e ![errfile]! -m n -l h_rt=![nsecs]!,h_vmem=![memgb]!G,mem_free=![memgb]!G,m_mem_free=![memgb]!G "
" > /dev/null