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Demultiplexing error #313

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erasche opened this Issue Oct 2, 2015 · 10 comments

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erasche commented Oct 2, 2015

cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git rev-parse HEAD
cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git diff --quiet
Repository hmmer_hmmemit updated successfully.
cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git rev-parse HEAD
cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git diff --quiet
Repository hmmer_hmmconvert updated successfully.
cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git rev-parse HEAD
cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git diff --quiet
Unexpected response from galaxy: 400: {"err_msg": "Enter the required repository name.", "err_code": 400008}
Repository [None] does not exist in the targeted Tool Shed.
cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git rev-parse HEAD
cd '/home/hxr/work/tools-iuc/tools/hmmer3' && git diff --quiet
Repository hmmer_nhmmscan updated successfully.

hard to tell which tool exactly produced that error.

@erasche erasche added the bug label Oct 2, 2015

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erasche commented Oct 2, 2015

Followed by:

Could not update suite_hmmer_3
Unexpected response from galaxy: 500: {"content_alert": "", "err_msg": "The repository_dependencies.xml file contains an invalid <repository> tag.  Unable to locate repository with name None and owner iuc.  "}
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erasche commented Oct 2, 2015

Okay, it's trying to include a macros.xml file.

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erasche commented Oct 2, 2015

Ignoring the macros.xml file in the .shed.yml produces a failure:

Unexpected response from galaxy: 500: {"content_alert": "", "err_msg": "Metadata may have been defined for some items in revision '5cbcb382871e'.  Correct the following problems if necessary and reset metadata.<br/><b>hmmemit.xml<\/b> - This file refers to a missing file <b>macros.xml<\/b>.  Upload a file named <b>macros.xml<\/b> to the repository to correct this error.<br/>"}

Seems like a bug in tool file discovery process.

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erasche commented Oct 8, 2015

@jmchilton where might I go about patching this? I'm not at all familiar with the demultiplexing and shed upload. Any pointers would be greatly appreciated :)

@erasche erasche referenced this issue Oct 8, 2015

Merged

Demultiplex the hmmer tools #307

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jmchilton commented Oct 11, 2015

Everything interesting I think happens below _realize_effective_repositories in the call stack - https://github.com/galaxyproject/planemo/blob/master/planemo/shed/__init__.py#L719. I'll try myself to find some time to look at this, since you know I promised I would.

@erasche erasche changed the title Demultiplexing error issue Demultiplexing error Oct 15, 2015

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jmchilton commented Oct 15, 2015

I know I promised to work on this, but I'm not sure it will be possible before mid November anymore, sorry. I have to get ready for Genome Informatics and Festival of Genomics so I should focus on Galaxy and workflows for the time being.

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erasche commented Oct 15, 2015

OK. Not a problem. Thanks for the update. khmer and hmmer updates are blocking on this, so maybe I'll find time for it soon.

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jmchilton commented Oct 15, 2015

Maybe a more pressing weekend project than Galaxy admin configuration documentation (snore) and more fun 😉.

@erasche erasche assigned erasche and unassigned jmchilton Oct 15, 2015

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natefoo commented Oct 16, 2015

Snore? The most exciting of weekend projects!

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erasche commented Oct 20, 2015

I've tracked it down to something that looks like a Galaxy bug.

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/loader_directory.py#L43

Is picking up tool_dependencies.xml because someone chose to write '<tool' instead of '<tool '. With that one character change, I can successfully demultiplex properly.

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