FreeBayes: installing onto local instance of Galaxy

I have a local instance of Galaxy 19.01.
From the ToolShed, I installed freebayes (156b60c1530f). When I ran it, the following error occurred:
Fatal error: Exit code 127 ()
/home/tecnico/galaxy/database/jobs_directory/003/3330/ riga 9: parallel: comando non trovato
To solve the problem, I also installed freebayes from the terminal on Ubuntu as follows:
sudo apt install freebayes
Now freebayes works even within Galaxy.
I found this procedure useful for other tools as well.

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it is a workaround …Galaxy manage tool dependencies through Conda and create for every tool a specific environment in /tool_deps/_conda/envs/ is better installing the missing package using Conda in the environment itself

Can you explain in detail how to do it?

this is the link to the official documentation
when the tool doesn’t work for a missing package I perform the following steps:

  • delete the Conda environment created by the tool
  • rerun the tool
    if the package is missed again:
  • activate the Conda environment ~$source _conda/bin/activate
  • enter in envs dir
  • activate the tool environment ~$source activate __samtools(ecc)
  • install missing packages with ~$conda install -c (conda channel: conda-forge or bioconda) (name_of the package)
  • rerun the tool
    yes is a bit difficult but:
    “Environments are of particular relevance when making bioinformatics projects reproducible. Full reproducibility requires the possibility to recreate the system that was originally used to generate the results. This can, to a large extent, be accomplished by using Conda to make a project environment with specific versions of the packages that are needed in the project” cit.
    and it is HPC-cluster ready :slight_smile:
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