Please follow the procedure described at https://github.com/galaxyproject/usegalaxy-playbook/wiki/Installation-on-Main (but use arguments for Test as described in the document).

You should not use this method except as a last resort.

Before you begin see Getting Set Up At TACC

Make sure nobody is running a docker container before restarting the docker service (e.g. with docker ps)...

$ ssh [email protected]
$ cvmfs_server transaction test.galaxyproject.org
$ docker run --rm -v /cvmfs:/cvmfs -p 127.0.0.1:8808:8888 galaxy/test_installer

Go to https://test-installer.galaxyproject.org/ and install tools as normal.

Conda can install things with less-than-world-readable permissions, which will cause the Galaxy user to be unable to read them, since the CVMFS client mounts everything as the cvmfs user. Additionally, it leaves behind tarballs (which Galaxy will complain about) and often fails to make conda/activate/deactivate symlinks in new environments.

Fix this with:

^C (to stop Galaxy)
$ /cvmfs/test.galaxyproject.org/bin/post_install.sh

Get the latest tag and append .N to the tag name, e.g. if latest tag is galaxy_16.04.04863c8, the new tag should be galaxy_16.04.04863c8.1, followed by galaxy_16.04.04863c8.2, etc.

$ cvmfs_server tag test.galaxyproject.org
$ cvmfs_server publish -a galaxy_16.04.04863c8.1 -m 'Installed/Updated Foo Tool' test.galaxyproject.org
$ logout

If the tool wrapper uses $GALAXY_SLOTS, edit env/test/templates/galaxy/config/job_conf.xml.j2 and add an entry for the tool to run on the multi partition, e.g. (copy from from other multi tools):

    <tools>
        ...
        <!-- resubmit to stampede jobs -->
        ...
        <tool id="SHORT_TOOL_ID" destination="dynamic_local_stampede_select_dynamic_walltime" handler="multi_handlers"  resources="local_or_stampede"/>
    </tools>

See the Getting Set Up At TACC page for the ansible-env function.

If a job_conf.xml change was not made, run:

$ ansible-env test snapshot
$ ansible-env test backup

If a job_conf.xml change was made, run:

$ ansible-env test snapshot --tags=no-restart
$ ansible-env test config

Inspect the mutable configs and push if everything looks good.

$ git diff     # verify that none of the mutable configs pulled to the playbook are mangled
$ git add -- .
$ git commit -m 'Update Test mutable configs'
$ git push