- Galaxy 19.01. I did not initially start it up in a virtualenv like the example, I let the run.sh script do that for me and I thought that was the same (If you do everything without conda). This was a different computer.
2.Galaxy 19.05. A fresh clone, no upgrade. I did not initially start it up in a virtualenv like the example, I let the run.sh script do that for me and I thought that was the same (If you do everything without conda).
- ubuntu 18.10
I just Create a new 18.10 ubuntu in virtualbox to test some options.
test1. Install git, install python2,create galaxy user, download galaxy, run galaxy.
When I execute a bash script containing
which python and run the tool I get
test2. download galaxy, install virtualenv, create .venv, run galaxy (like the example).
Same result as test1.
I can overcome this by giving the full path of the python that I want, and 99,99% I wil use the python of a conda environment anyways but this behavior that I do not expect worry’s me for the stability in the future.
test3. For this test I use the galaxy of test2. But I let galaxy install conda for me in the folder /opt/conda/anaconda3. The /opt/conda folder has full permission (chmod 777). I test if conda works by installing and uninstalling dependencies in the manage dependencies screen.
Galaxy and conda work so all good, except that it is still not using the PATH of my system.
test4 I use the galaxy of test 3 but give full rights (chmod -R 777 /opt/conda) to conda.
Everything still works
test5 this time I change the owner of all the files in /opt/conda. (chown -R otheruser /opt/conda)
Everything still works
test6 For this test I will use the galaxy of test1 but I install conda manually in /opt/conda/anaconda3_2 with user galaxy. If I install a dependency conda is working and is actually installing the dependencies. Also if I do
/opt/conda/anaconda3_2/bin/conda env list I see them but galaxy can not find them after installation. In my terminal after installation in see many
Dependency not found errors. I tried to set
conda_prefix: /opt/conda/anaconda3_2/envs but this also did not work.
Galaxy is not using the PATH of my system.
Galaxy can use my manually installed conda but after installing a dependency I get many
Dependency not found errors