planemo test/serve conda package installation

1

Hi there,

I’m trying to test a wrapper with Planemo on my local computer.

  • planemo version: 0.75.27
  • galaxy version: release_24.2
  • wrapper depends on curl, gzip, python-libsbml, requests, taxonid and call a piece of Python code in command section
  • running within both _galaxy_ and fresh dedicated planemo conda envs on macOS 15.3.2

The command planemo test --galaxy_root=<path>/galaxy my_wrapper.xml raises the following error in tool_test_output.json:

from libsbml import readSBMLFromFile
ModuleNotFoundError: No module named 'libsbml'

Error ModuleNotFoundError: No module named 'taxonid' raises if I put import taxonid first in the Python code called by the wrapper.

The command planemo serve --galaxy_root=<path>/galaxy my_wrapper.xml raises the following one:

Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

  - taxonid

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch

Same for requests, although both exist on conda-forge/noarch.

Any help would be very appreciated. Thank you!

"Job in error state.." Planemo Test Error Message
2

Ok, the source of the issue was that Galaxy (through planemo command) uses $HOME/miniconda3 as conda path and this folder already existed on my computer with an old version of conda. Removing this folder led Galaxy to recreate a new miniconda folder with a fresh version of conda and the current issue just gone, i.e. packages libsbml and taxonid have been installed properly.

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