Can we just merge this now?

No, but maybe if I get some time later today I can finish it.

@jmchilton Is there anything special I should do wrt. updating the Galaxy lib? I could just remove the eggs stuff, but it feels more correct to just copy the relevant things directly from Galaxy so they are the latest versions, but obviously you must have done that with modifications to wrap the eggs imports in the past.

One other thing... would $GALAXY_HOME even be necessary for anything going forward if we:

1. Included Galaxy's galaxy_ext module in Pulsar
2. Documented how to specify a venv to use for running tools
3. Documented which tools shipped with Galaxy depend on things in that venv - @nsoranzo's work in Remove remaining references to galaxy.eggs . flake8 some tools. galaxy#990 should make this easy

GALAXY_HOME necessary because metadata depends on models and datatypes.

There is a script for synchronizing - see update_galaxy_client.sh and update_galaxy_utils.sh in PULSAR_ROOT.

update_galaxy_utils.sh pulls $GALAXY/lib/galaxy/job/runners/util into $PULSAR/pulsar/managers/util, but the Pulsar copy has modifications that Galaxy does not have. Should Pulsar be the canonical source for this, or Galaxy?

• $PULSAR/pulsar/managers/util
• $GALAXY/lib/galaxy/jobs/runners/util

I can correct it (which will just mean merging them) but just wanted to know. Perhaps a README in the downstream directory indicating that changes need to be made upstream and then synchronized would be a good idea.

@jmchilton

Galaxy seems to be missing things that Pulsar has that came from Planemo?:

• $PULSAR/galaxy/tools/linters/stdio.py
• $PULSAR/galaxy/tools/linters/xml_order.py
• $PULSAR/galaxy/tools/linters/xsd_util.py

Should these be synchronized Planemo -> Galaxy -> Pulsar? Any others like this I need to watch out for?

Merged with @nsoranzo two fixes.