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various fixes #9

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merged 2 commits into from Feb 20, 2020
Merged

various fixes #9

merged 2 commits into from Feb 20, 2020

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bgruening
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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)

bgruening
bgruening commented Feb 20, 2020
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tools/hyphy/macros.xml Outdated
<option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
</param>
<when value="Variational-Bayes">
<expand macro="mcmc_options" />
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This one I'm not sure, are the mcmc options needed in variatianal-bayes or in metropolis-hastings?
You if condition below was indicating #if $posteriorEstimationMethod.method != "Metropolis-Hastings" but I'm not sure.

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MCMC options are not needed for Variational Bayes; are needed for the other two

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From the code it looks like the MCMC options are irrelevant if variational-bayes is selected, so the if statement needs to be updated.

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Yes, it does need to be updated.

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This brings down the errors to only one.

done ; ln -s '/tmp/tmpdnsRsD/files/9/6/0/dataset_9608cc9b-f33b-43f2-b05f-2ad26fb3970e.dat' gard_input.fa && ${GALAXY_MPIRUN:-mpirun -np ${GALAXY_SLOTS:-1}} HYPHYMPI gard --alignment ./gard_input.fa --type 'nucleotide' --output '/tmp/tmpdnsRsD/files/0/8/6/dataset_086ccd89-23a5-4c39-ad0b-3d68b7703450.dat' --output-lf '/tmp/tmpdnsRsD/files/5/d/c/dataset_5dcb4f81-b644-460e-8461-c4a7e0388c76.dat' > '/tmp/tmpdnsRsD/files/c/b/3/dataset_cb3f65ee-8879-45c6-b870-ae4670f88e59.dat']
2020-02-20 12:06:14,454 INFO  [galaxy.tool_util.output_checker] Job 8: {'code_desc': '', 'error_level': 3, 'type': 'exit_code', 'exit_code': 1, 'desc': 'Fatal error: Exit code 1 ()'}
FAIL

No real error message, seems the tool crashed?

@davebx davebx requested a review from spond February 20, 2020 12:17
@davebx
Exclude MCMC from Variational-Bayes.
09695dd 
Per tool author: "Variational-Bayes only uses the grid option and the concentration parameter option. It is an iterative deterministic method"
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davebx commented Feb 20, 2020

With a patch to GARD.bf everything runs correctly now

@davebx davebx merged commit 5375187 into davebx:hyphy_254 Feb 20, 2020
@bgruening bgruening deleted the fixes-hyphy branch February 20, 2020 18:17
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@davebx davebx davebx approved these changes

@spond spond Awaiting requested review from spond

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@bgruening @davebx @spond