Pulsar Galaxy Lib

0.15.14 verified Mon Apr 27 auth: no python

Distributed job execution application built for Galaxy (http://galaxyproject.org/). Current version 0.15.14. Release cadence irregular; minor versions every few months.

pip install pulsar-galaxy-lib

Common errors

error ImportError: No module named 'pulsar' ↓

cause Installed wrong package (e.g., 'pulsar' not 'pulsar-galaxy-lib').

fix

pip uninstall pulsar && pip install pulsar-galaxy-lib

error pulsar.client.PulsarClientError: 403 Forbidden ↓

cause private_token mismatch between client and server.

fix

Verify the server's 'private_token' in config and pass the same token to PulsarClient.

error pulsar.app.ManagerApp requires a valid persistence backend ↓

cause No Redis or database URL configured in app object.

fix

Set app['redis_url'] = 'redis://localhost:6379/0' or app['database_url'] = 'sqlite:///pulsar.db'.

Warnings

gotcha Pulsar requires a Redis or database backend for job management. Without it, jobs may not persist or recover. ↓

fix Configure app['redis_url'] or app['database_url'] in the app config.

gotcha The 'private_token' must match the server's 'private_token' config. Mismatch leads to 403 errors. ↓

fix Ensure tokens are identical on client and server side.

gotcha When using DRMAA or Condor, job cleanup may leave orphaned processes if not configured properly (see 0.15.13 changelog). ↓

fix Update to latest version and set 'cleanup_jobs = always' in the manager config.

gotcha The library 'pulsar-galaxy-lib' on PyPI is separate from the 'pulsar' package. Install the correct one. ↓

fix pip install pulsar-galaxy-lib (not 'pulsar')

Imports

ManagerApp

wrong

from pulsar import ManagerApp

correct

from pulsar.app import ManagerApp

Import from pulsar.app, not top-level pulsar

PulsarClient

wrong

from pulsar import PulsarClient

correct

from pulsar.client import PulsarClient

Import from pulsar.client submodule

PulsarServer

wrong

pulsar.PulsarServer

correct

from pulsar.server import PulsarServer

Full import path from pulsar.server

Quickstart

Create a Pulsar client and submit a basic job.

from pulsar.client import PulsarClient

client = PulsarClient('http://localhost:8913', private_token='secret')
# Submit a simple job
client.submit_job({
    'command_line': 'echo hello',
    'tool_id': 'echo_tool',
    'inputs': {},
    'outputs': {},
    'output_collections': []
})