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Fix ktImportText dependency for krona_text #900

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jennaj opened this issue Dec 17, 2024 · 0 comments
Open

Fix ktImportText dependency for krona_text #900

jennaj opened this issue Dec 17, 2024 · 0 comments
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bug Something isn't working site/org usegalaxy.org

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@jennaj
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jennaj commented Dec 17, 2024

toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1

ktImportText: command not found

Fails at ORG, works at EU
Test data history https://usegalaxy.org/u/jen-galaxyproject/h/imported-from-archive-test-krona-tools
Reported at https://help.galaxyproject.org/t/visualize-with-krona/14111/ (thanks!)

Workaround for end users until resolved

  1. Choose a different Krona tool to use, example Krona pie chart from taxonomic profile (link at ORG)
  2. Or, transfer your dataset or entire history over to the EU server and work there instead for this step.

Job Information

Galaxy Tool ID toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1
Job State error
Command Line bash /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/b14f1444e464/krona_text/runKrona.sh /jetstream2/scratch/main/jobs/63653172/inputs/dataset_736db9f9-a11a-48b5-ba5d-b6c89a21b20c.dat N /jetstream2/scratch/main/jobs/63653172/outputs/dataset_1d3c6d9c-96d8-4eee-97df-77ef68c5b8cb.dat
Tool Standard Output starting 100.0 unclassified 100.0 unclassified /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Tool Standard Error /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/b14f1444e464/krona_text/runKrona.sh: line 27: ktImportText: command not found
Tool Exit Code 127
Job API ID bbd44e69cb8906b5688377bda9605ecc (63653172)
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