User: esch0041

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esch004160
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Posts by esch0041

<prev • 8 results • page 1 of 1 • next >
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planemo test - mysterious samtools dependency
... When I run planemo test for a tool that has declared no dependencies on samtools, I nevertheless see the following in the output > 2018-01-08 19:01:58,214 DEBUG [galaxy.tools.deps] Building dependency shell command for dependency 'samtools' > 2018-01-08 19:01:58,215 DEBUG [galaxy.tools.deps] ...
planemo written 7 days ago by esch004160 • updated 6 days ago by jmchilton1.0k
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Answer: A: toolshed repository - "This revision can be installed: False" - why?
... I don't see anything in the [XML reference for comments][1] saying that they cannot appear outside the root element. Planemo serve, test, lint and shed_lint all worked fine with my tool definition XML, which ended with an XML comment that serves as a "vim modeline". Vim modelines are instructions ...
written 8 months ago by esch004160
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Comment: C: toolshed repository - "This revision can be installed: False" - why?
... Thanks, Bjoern. Indeed the files are present in the repository on the testtoolshed (when I browse tip and when I hg clone), but even after shed_upload it is still marked `This revision can be installed: False`. Looking at other tools, I cannot spot what I am missing in my repository. ...
written 8 months ago by esch004160
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toolshed repository - "This revision can be installed: False" - why?
... I built a tool that passed `planemo test` and `planemo shed_lint`, and I deployed it to a testtoolshed repository using `planemo shed_create` with [the .shed.yml here][1]. When I look at it in the test toolshed [w4mclassfilter][2] the repository browser says "This revision can be installed: False". ...
toolshed written 8 months ago by esch004160
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Comment: C: Planemo tutorial test - "Failed to resolve dependency" "Error loading a set of D
... Martin, Thank you very much for your response. What a difference a few days make! Now, when I run with the same command as before, I still see most or all of the warnings and errors, but my test passes. Granted, I did this with a new virtualenv. I did it outside the VM; previously, my test failed ...
written 19 months ago by esch004160
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Comment: C: Capsule with dependencies - "dependency hierarchy could not be determined"
... I tried resetting the repository metadata for each repository, one at a time. As far as I can tell, this seems to have been effective - I saw no errors when I installed package_r_3_2_1 into my repository. ...
written 19 months ago by esch004160
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Planemo tutorial test - "Failed to resolve dependency" "Error loading a set of Dynamic Display Application links"
... I have been trying to follow the tutorial ["The Basics" under "Building Galaxy Tools ... using Planemo][1] and I have been getting. When I run >` planemo test --install_galaxy --test_output test-output/test_output.dat --test_data test-data/ seqtk_seq.xml` my test fails, and I see several WARN ...
planemo test test dependency planemo written 19 months ago by esch004160 • updated 19 months ago by Martin Čech ♦♦ 4.3k
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Capsule with dependencies - "dependency hierarchy could not be determined"
... I have exported package_r_3_2_1 as a capsule including dependencies from https://toolshed.g2.bx.psu.edu/repository?repository_id=9d4c4c6c8e05e067&changeset_revision=d9f7d84125b7 and imported it into a freshly created local tool shed. When I preview package_r_3_2_1 for installation to my freshly ...
galaxy capsule dependencies tool shed written 19 months ago by esch004160

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Scholar 8 months ago, created an answer that has been accepted. For A: toolshed repository - "This revision can be installed: False" - why?

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