search

usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
0 stars 0 forks source link

Barplot fails #58

Closed ehj000 closed 2 years ago

ehj000 commented 2 years ago

This error looks familiar. Anyone knows how to fix this: gnuplot: error while loading shared libraries: libGL.so.1: cannot open shared object file: No such file or directory

kjetilkl commented 2 years ago

This tool only has one listed requirement: gnuplot-py (which also depends on gnuplot) I tried to build the container manually but got the same error. However, when I placed Bioconda before Conda-forge in the channels list and tried building it again, it complained about missing the shared library libjpeg.so.8 instead. The gnuplot-py container in BioContainers has similar issues, so using that didn't work either. Finally, I managed to solve it by adding a symlink from the file libjpeg.so.9 to libjpeg.so.8 inside the container. At least you now get plots that are just as ugly as those made by UseGalaxy.eu, but even though output is produced, the job ends in a red error state since the tool complains about a missing font to STDERR. This could probably be suppressed to get a green job state instead, but that will require modifications to the tool wrapper.

kjetilkl commented 2 years ago

I hacked the "bar_chart.xml" tool wrapper (which comes bundled with Galaxy in the "tools/plotting" directory) and added a profile="16.04" attribute to the <tool> element. This ensures that Galaxy no longer automatically treats output to STDERR by this tool as a sign of failure. However, since the hack was done directly in Galaxy code, I'm not sure if it will persists, and a better solution is desirable. Also, the font is still ugly (but similar to UseGalaxy.eu).

ehj000 commented 2 years ago

The tools works, and yes, the plots are not eye candy. Thanks again Kjetil