Error trying to build docs locally

[Michael Hall]

When trying to build the docs locally I get the following error

Exception occurred:
  File "/home/vagrant/Projects/snakemake-wrappers/docs/generate_docs.py", line 50, in render_wrapper
    with open(os.path.join(path, "test", "Snakefile")) as snakefile:
FileNotFoundError: [Errno 2] No such file or directory: '/home/vagrant/Projects/snakemake-wrappers/bio/gatk3/indelrealigner/test/Snakefile'
The full traceback has been saved in /tmp/sphinx-err-l5dcckmy.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.

Looks like it is expecting a test Snakefile for gatk3 indelrealigner but there doesn't seem to be one.

[Michael Hall]

The fact that there is no test seems to have been acknowledged by @Smeds in https://bitbucket.org/snakemake/snakemake-wrappers/pull-requests/64/wrappers-for-gatk3-tools/diff

Is there a way to either skip the build of these docs? Maybe we could just create a dummy test Snakefile?

[Michael Hall]

Actually, given that none of the sub-wrappers for gatk3 have tests then the error will obviously occur for all the sub-wrappers. This also leads to there being no docs for gatk3 on the website...

[Patrik Smeds]

I added test/Snakefile for the gatk3 wrappers (68) and now the doc build. I haven't added them to test.py since they will fail due to missing gatk3-jar.

[Johannes Köster]

Fixed by merging the PR. Thanks guys!