Allow specification of environment variables for job destinations

#378 Merged at 4d554f1
Repository
galaxy-central-fork-1
Branch
default
Repository
galaxy-central
Branch
default
Author
  1. John Chilton
Reviewers
Description

See modification to job_conf.xml.sample_advanced for description of how to set environment variables. Should work for all runners except local and CLI (same restrictions as job metrics). Both of these limitations will be lifted once local and CLI runners are ported to use the job_script module.

For more discussion and motivation see this galaxy-dev thread and this Trello card.

This pull request differs from the original patch that I attached in that it will attempt to auto quote environment variables (unless explicitly disabled by setting raw to true), works with the LWR (with any LWR backend - up-to-date LWR required), and includes tests (unit tests here - but LWR includes full integration tests with many different backends that verifies this functionality).

Updated 4/24 - Added <env file="/path/to/source" /> and <env exec="cmd --to --execute"> options.

Comments (1)