I work on galaxy dev, and I want use conda with it.
My tools I want use are in python 2.7 this is why I need to configure conda.
I want create a docker version of this galaxy.
I have a external postgress server already configured, this is why I don’t want use the official docker version of galaxy.
My conda version are the last version of the official repo: https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main
dependency_resolvers_config_file: config/dependency_resolvers_conf.xml (I use the original sample)
conda_exec: /opt/conda/bin/conda (I have a symbolic link: ln -s /opt/conda/bin /home/galaxy/.conda/)
After the installation galaxy work fine, and I can use external commands of conda.
The first problem are a problem of installation of dependency. Galaxy use this command:
/opt/conda/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel iuc --channel defaults --channel R --name mulled-v1-5b73db27209dd7e83d26bd4dedeadbcf356c9297c08644dec23df66a734a236c python=2.7 scipy matplotlib Pillow reportlab tk ConfigParser
But we obtain no output, and the conda env are not create and when I use it with the galaxy user, it create the environment. I don’t understand why.
After the creation of the environment galaxy detect it and want use it. But, when it activate it, the environment are not correctly initialize and I obtain this error:
Traceback (most recent call last):
File “/home/galaxy/tools/ngs-qc/galaxy.py”, line 11, in
File “/home/galaxy/tools/ngs-qc/gviewer.py”, line 11, in
ModuleNotFoundError: No module named ‘ConfigParser’
And when I check the version: 3.6.13 | packaged by conda-forge
This is the version of my galaxy env, not the version for my tool.
What do you think I have to change in my config ?
In advance, thank you for your help.