add refgenie pull to data managers

[nvk747]

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[blankenberg]

This will be hard to test currently, as it requires the installation and configuration of refgenie. Quick couple of options:

1. Have test harness include a refgenie configuration file and set in galalxy config.
2. Skip tests for this data manager
3. Hack in behavior so that a missing config value runs green/'ok' but doesn't fetch data., or some other workaround just for tests to pass.

I lean towards 2 right now.

3. just seems like a bad idea. 1 seems heavy-weight requiring changes outside of the tool, but would be good -- only really need to create a temp. dir and place a yaml file in there, pass yml filepath to Galaxy config.

Thoughts?

[bgruening]

Have test harness include a refgenie configuration file and set in galalxy config.

planemo can setup Galaxy's with a specific configuration. We could integrate a refgenie mode in planemo and make sure this works.

[blankenberg]

Hopefully galaxyproject/planemo#1025 allows this test.

[bgruening]

ok, your PR should be in the latest release :)

[bgruening]

I merged master into this one and triggered a test.

[nvk747]

Does anyone have any questions, concerns, or suggestions for this pull request?

[blankenberg]

Digging into this locally, it looks like the issue is being caused due to the tool running inside of a container that does not have access to the planemo created temporary refgenie genome_config.yml.

Config file path isn't a file: /tmp/tmpvnrdbrfs/refgenie/genome_config.yaml
Traceback (most recent call last):
File "/usr/local/bin/refgenie", line 10, in <module>
sys.exit(main())
File "/usr/local/lib/python3.8/site-packages/refgenie/refgenie.py", line 659, in main
rgc = RefGenConf(filepath=gencfg, writable=False)
File "/usr/local/lib/python3.8/site-packages/refgenconf/refgenconf.py", line 77, in __init__
super(RefGenConf, self).__init__(filepath=filepath, entries=entries, writable=writable, wait_max=wait_max)
File "/usr/local/lib/python3.8/site-packages/yacman/yacman.py", line 84, in __init__
file_contents = load_yaml(filepath)
File "/usr/local/lib/python3.8/site-packages/yacman/yacman.py", line 362, in load_yaml
with open(filepath, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpvnrdbrfs/refgenie/genome_config.yaml'

Works well and tests pass when run outside of the planemo launched tool container.

Thoughts on how to inform the tests to mount the needed files into the tool container? Or how to otherwise proceed? Thanks!

[blankenberg]

For testing locally:

this works

planemo test data_managers/data_manager_refgenie_pull/data_manager/data_manager_refgenie_pull.xml 

this does not

planemo test --biocontainers --no_dependency_resolution --no_conda_auto_init data_managers/data_manager_refgenie_pull/data_manager/data_manager_refgenie_pull.xml