Persistent import postgres fix, data managers and dataset purge

ARTbio / GalaxyKickStart

Ansible playbooks for Galaxy Server deployment

GNU General Public License v3.0

24 stars 22 forks source link

Persistent import postgres fix, data managers and dataset purge #119

Closed mvdbeek closed 8 years ago

mvdbeek commented 8 years ago

Persistent import postgres fix
Include data managers for bowtie, bowtie2 and fasta in metavisitor tool list. The order of the tools is slightly re-arranged (ordered alphabetically), because I used the get_tool_tool_yml_from_gi.py script on an instance where I manually installed those data managers.
Allow users to delete files via UI
Add ../shed_tools/ directory to list of directories that need to persist.

Closes #115 #116 #117 #118

mvdbeek commented 8 years ago

I have tested this on @drosofff's instance on the IFB cloud. What was missing was the shed_tools directory. To "fix" your instance, I deleted the /export/exported_dirs.yml file (we use the presence of this file to check if we should export or not) and ran the last command from the Dockerfile again:

ansible-playbook galaxy.yml -c local --tags "persists_galaxy,nginx_config,galaxy_config_files,galaxy_extras_job_conf" --skip-tags=skip_supervisor_start_in_docker \
           --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION \
           --extra-vars galaxy_admin=$GALAXY_CONFIG_ADMIN_USERS -i docker_inventory

This caused the /home/galaxy/shed_tools directory to appear in /export/home/galaxy/shed_tools. So if you shutdown this instance and start it again, you should have all the custom-installed tools still installed (but I didn't test it).

drosofff commented 8 years ago

There is progress... but the data manager and their tables which I manually installed on the instance when data were persisted are still missing.

mvdbeek commented 8 years ago

but the data manager and their tables which I manually installed on the instance when data were persisted are still missing.

When did you install those ? After I added my last comment to this PR?

mvdbeek commented 8 years ago

OK, it was sufficient to re-install the data managers, then you get the reference data back automatically. The shed_tools directory contains for example shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/e87aeff2cf88/data_manager_bowtie2_index_builder. With the command I posted above we were copying what was present in the image to the correct location, but that didn't include the manually installed tools (which were not present in /export/home/galaxy/shed_tools/...), so that's why your data managers were not present, even though the tools that were installed when we build the image were present.

drosofff commented 8 years ago

👍 👍