Soft-link run_ilastik.sh in conda bin directory

[drpatelh]

Hi. I was wondering whether it would be possible to soft-link the run_ilastik.sh script in the environment bin/ directory as part of the recipe build process. Currently, it is placed in the top-level directory of the conda environment. I have tested this behaviour after the creation of the conda environment and it works well. I think I remember having issues when the script was physically copied in bin/ due to path searches.

I am trying to run ilastik as part of a pipeline in --headless mode, and ideally I dont want to have any interaction with the environment other than sourcing it:
https://github.com/drpatelh/nf-core-imcyto/blob/master/environment_ilastik.yml

In my opinion this would make things more portable across multiple containers so it would be great to know what you think.

[k-dominik]

If you are using conda anyhow, there is no need to go via run_ilastik.sh. You can then safely just call python ilastik-meta/ilastik/ilastik.py.

run_ilastik.sh is there to start ilastik when distributed in binary form