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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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workflows tests fail on v6 #1255

Closed ShaiberAlon closed 4 years ago

ShaiberAlon commented 4 years ago

So far it looks to me like the only issue is the new HMMs, I relied on Campbell_et_al to test the phylogenomics workflow, and I need to switch to the new HMMs.

The issue is that in my mock dataset each contigs database only has a single HMM hit with this collection (and all of these are identical AAs). I need to update the FASTA files and add at least one more gene from the new HMM collection.

Also need to fix the relevant config files: sandbox/workflows/phylogenomics/config.json sandbox/workflows/pangenomics/pan-config-with-phylogeny-using-hmms.json

ShaiberAlon commented 4 years ago

Closed by: https://github.com/merenlab/anvio/commit/80f136b09da96e3f670dd0f7f2e0b7b923fdcde1 https://github.com/merenlab/anvio/commit/fa8e813dbe9c4c75bdb1269e787ff04bd14eaae7 https://github.com/merenlab/anvio/commit/30fbe7d024c86566a2178d03f4e8bbf388b868fa https://github.com/merenlab/anvio/commit/de360890a1b9b2f9444efa3c0f9a50b53fc47049 37d4765c6c0448b696f0e86affd92f0fe96a0e9f b07afd72a888c4143c9f4e17d32408ad987676d5 f889adf3fe60254a7c44081726b55573696ab089

(don't ask me why I didn't do all these on a branch. I should have.)

Most of these changes are in the test package, but there were some minor bug fixes too.

@meren, all the tests in anvio/tests/run_workflows_tests.sh are now working on master.

If you get a chance to also run it on your computer (just as a sanity check) that would be great (but take into account that it takes 10-20 minutes to run since it is a lot of tests and includes full workflows with different configs).