http://g2.trac.bx.psu.edu/browser/lib/galaxy/jobs/runners/pbs.py?rev=1696%3Aaac0403bbe68
Code
199 # write the job script
200 if self.app.config.pbs_stage_path != '':
201 script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames()), self.app.config.pbs_stage_path, exec_dir, command_line)
202 else:
203 script = pbs_template % (job_wrapper.galaxy_lib_dir, exec_dir, command_line)
204 job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
205 fh = file(job_file, "w")
206 fh.write(script)
207 fh.close()
.
.
# submit
218 galaxy_job_id = job_wrapper.job_id
219 log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) )
220 log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) )
221 job_id = pbs.pbs_submit(c, job_attrs, job_file, pbs_queue_name, None)
222 pbs.pbs_disconnect(c)
从此 例可看出 脚本文件 *.sh 是 在 C程序中动态生成的.
