SMRT Service commandline interface¶

A high level client to the SMRT Link Services is accessible from ServiceAccessLayer in pbcommand.services.

Client Layer¶

Example:

In [1]: from pbcommand.services import ServiceAccessLayer

In [2]: s = ServiceAccessLayer("smrtlink-alpha", 8081)

In [3]: s.get_status()
Out[3]:
{u'id': u'smrtlink_analysis',
 u'message': u'Services have been up for 141 hours, 37 minutes and 13.138 seconds.',
 u'uptime': 509833138,
 u'user': u'secondarytest',
 u'uuid': u'12e1c62a-99a4-46c1-b616-a327dc38525f',
 u'version': u'0.1.8-3a66e4a'}

In [4]: jobs = s.get_analysis_jobs()

In [5]: j = s.get_analysis_job_by_id(3)

In [6]: j.state, j.name
Out[6]: ('SUCCESSFUL', 'sirv_isoseq')

In [7]: import pbcommand; pbcommand.get_version()
Out[7]: '0.4.9'

Commandline Tool Interface to Services¶

Warning

This has been migrated to scala in smrtflow. Support for the python Client layer API will remain, however the python commandline tool is no longer installed by default and will be removed in a future version.