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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Multiple tools in AmrPlusPlus pipeline fails with similar error #50

Closed ehj000 closed 2 years ago

ehj000 commented 2 years ago

The tools "SNPFinder" (https://usegalaxy.no/root?tool_id=toolshed.g2.bx.psu.edu/repos/chrisd/snpfinder/snpfinder/0.1.0), "RarefactionAnalyzer" (https://usegalaxy.no/root?tool_id=toolshed.g2.bx.psu.edu/repos/chrisd/rarefaction_analyzer/rarefaction_analyzer/0.1.0) and "ResistomeAnalyzer" (https://usegalaxy.no/root?tool_id=toolshed.g2.bx.psu.edu/repos/chrisd/resistome_analyzer/resistome_analyzer/0.1.0) all fails with the error.

Example for SNPFinder: /data/part0/tmp/jobs/000/107/107724/tool_script.sh: 9: /data/part0/tmp/jobs/000/107/107724/tool_script.sh: snpfinder: not found

All tools were installed when installing the complete AmrPlusPlus pipeline (http://megares.meglab.org/amrplusplus/latest/html/installation.html), and re-installed from the toolshed without any positive effect.

ehj000 commented 2 years ago

The new containers Kjetil buildt for SNPFinder, ResistomeAnalyzer and Rarefaction is working fine. Thanks