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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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The "Visualize with Krona" tool fails because the perl interpreter is missing #85

Closed kjetilkl closed 2 years ago

kjetilkl commented 2 years ago

The "Visualize with Krona" tool (ID: krona_text) fails with the following error:

/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/b14f1444e464/krona_text/runKrona.sh: /usr/local/bin/ktImportText: /usr/bin/perl: bad interpreter: No such file or directory
kjetilkl commented 2 years ago

The tool runs in the container krona-tools:2.6 which actually includes a Perl interpreter in /usr/local/bin/perl, but all the scripts have hardcoded the path to /usr/bin/perl. We also have a container called krona:2.7.1--pl526_4 that includes the same scripts but without hardcoded paths. I assume that these versions are quite similar, so I just turned krona-tools:2.6 into a symlink which points to krona:2.7.1--pl526_4. (The old file was renamed to krona_tools_not_working:2.6.1). The tool then worked fine after I added it to the "allowlist" to render the HTML output correctly.