HTSeqCountCluster.pbsjob package

Submodules

HTSeqCountCluster.pbsjob.pbsconfig module

Configuration dictionaries for SGEJob class.

HTSeqCountCluster.pbsjob.pbsjob module

class HTSeqCountCluster.pbsjob.pbsjob.BasePBSJob(base_jobname)

Bases: object

Base class for simple jobs.

debug(code)

Debug the SGEJob.

class HTSeqCountCluster.pbsjob.pbsjob.PBSJob(email_address, base_jobname=None)

Bases: HTSeqCountCluster.pbsjob.pbsjob.BasePBSJob

Create a qsub/pbs job & script for the job to execute.

submit_cmd(cmd, cleanup=True)

Create and submit a qsub job.

Submit python code.

submit_code(code, cleanup=True, default=True)

Create and submit a qsub job.

Submit python code.

HTSeqCountCluster.pbsjob.pbsutils module

Collection of tools for using PBS, a job scheduler for high-performance computing environments. The command is usually qsub <options> on most systems.

HTSeqCountCluster.pbsjob.pbsutils.basejobids(length, name='submit')

“Create base job id and name.

Parameters:

• length ([type]) – [description]
• name (str, optional) – [description], defaults to ‘submit’

Returns:

[description]

Return type:

[type]

HTSeqCountCluster.pbsjob.pbsutils.file_to_str(filepath)

Turn the contents of a file (python file) into a string.

Parameters:filepath ([type]) – [description]

HTSeqCountCluster.pbsjob.pbsutils.import_temp(filepath)

Import a template file that has template strings.

Parameters:filepath ([type]) – [description]

HTSeqCountCluster.pbsjob.pbsutils.random_id(length=5)

Generate a random ID of 5 characters to append to qsub job name.

HTSeqCountCluster.pbsjob.pbsutils.write_code_file(filename, code, language)

Create a python file and write the code to it.

HTSeqCountCluster.pbsjob.qstat module

Access qstat information about SGE jobs.

class HTSeqCountCluster.pbsjob.qstat.Qstat

Bases: object

all_job_ids()

Retrieve a list of all jobs running or queued.

all_queued_jobs()

Retrieve a list of queued jobs.

all_running_jobs()

Retrieve a list of running jobs.

myjobs()

Retrieve a list of all the current user’s jobs.

qstatinfo(qstat_path='qstat')

Retrieve qstat output.

Parameters:qstat_path (str, optional) – [description], defaults to ‘qstat’

watch(job_id)

Wait until a job or list of jobs finishes and get updates.

Module contents