FreeBayes: installing onto local instance of Galaxy

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1

I have a local instance of Galaxy 19.01.
From the ToolShed, I installed freebayes 1.1.0.46 (156b60c1530f). When I ran it, the following error occurred:
Fatal error: Exit code 127 ()
/home/tecnico/galaxy/database/jobs_directory/003/3330/tool_script.sh: 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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2

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

3

Can you explain in detail how to do it?

4

this is the link to the official documentation https://docs.galaxyproject.org/en/master/admin/conda_faq.html
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. https://nbis-reproducible-research.readthedocs.io/en/latest/conda/
    and it is HPC-cluster ready :slight_smile:
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