Muliplex tissue imaging tools fail with dependency errors

[kjetilkl]

The newly installed imaging tools Process single-cell intensities and Rename OME-TIFF Channels both fail with the error:

Traceback (most recent call last):
  File "/data/part0/tmp/jobs/000/246/246977/configs/tmpmwa3i94a", line 4, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'

[kjetilkl]

The tools specify the following requirement for a Docker container:

<requirements>
    <container type="docker">quay.io/goeckslab/mti_utils:0.0.1</container>
</requirements>

I'm does not look like this way of specifying requirements works on UseGalaxy.no, since test jobs were executed with the default container.

To fix it, I manually downloaded the Docker container and converted it into a Singularity image, which I placed in /srv/galaxy/containers/singularity/mti_utils.sif. I then manually hacked the two installed tool wrappers:

• /srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/09e240a12897/rename_tiff_channels/macros.xml
• /srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/goeckslab/cell_intensity_processing/7a77ed0e579a/cell_intensity_processing/macros.xml

and changed the requirements to point to the new Singularity image file instead

<requirements>
    <container type="singularity">/srv/galaxy/containers/singularity/mti_utils.sif</container>
</requirements>