def build_qsub(self):
"""
Builds and writes this CallObject's qsub script to current working directory
using options provided under the "qsub_options" sub-tree in the yaml config file.
"""
nicknames = {'tophat':'th',
'cufflinks':'cl',
'cuffmerge':'cm',
'cuffdiff':'cd',}
qsub_options = self.yargs.qsub_options
# set keyword args for template
kw = Bunch()
kw.queues = qsub_options.queues
kw.datahome = qsub_options.datahome
kw.core_range = qsub_options.core_range
kw.email_addy = self.email_info.email_to
kw.call_id = self.call_id
job_name = "%s_%s" % (nicknames[self.prog_name], '_'.join(self.call_id.split('_')[1:]))
kw.job_name = job_name
kw.out_dir = self.out_dir
kw.ld_library_path = qsub_options.ld_library_path
# need to make sure we use the number of cores that the SGE gave us
kw.cmd_str = self.cmd_string.replace('-p %s' % (self.opt_dict['p']),'-p $CORES')
qsub_template = Template(filename=qsub_options.template)
out_file = open('%s.qsub.sh' % (self.call_id),'w')
qsub_string = qsub_template.render(**kw)
out_file.write(qsub_string)
out_file.close()
