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emo-bon / MetaGOflow

MGnify oriented implementation for the Marine Genomic Observatories oriented pipeline, developed in the framework of an EOSC-Life funded project
https://metagoflow.readthedocs.io
Apache License 2.0
7 stars 8 forks source link

refactoring and improve description of running the workflow and envir… #24

Closed jprmachado closed 1 year ago

jprmachado commented 1 year ago

Aim to improve the instructions to install and run the worflow

Open for discussion and help

hariszaf commented 1 year ago

Thanks a lot @jprmachado ! I cannot say much on this, it's mostly @steninidak part. I could only review in terms of polishing :stuck_out_tongue_winking_eye:

However, this is an essential PR so let us all give it a thorough look!

hariszaf commented 1 year ago

@jprmachado we need also the rocrate library

pip install rocrate

would work i guess.

Reg tabix I am not sure if it's a dependency.. Could you make sure of that ?

Thanks a lot!

jprmachado commented 1 year ago

@hariszaf @steninidak From what I see tabix is used in some scrips e.g. antimash_to_gff.py but all the scripts that I see are running inside the containers, so I guess the end user don't need tabix. scripts_python3/Dockerfile install tabix.

Futhermore those scripts include lines like if not args.no_tabix . So I guess is only needed inside the containers and even so it's does not lead to an interruption, just to files less compressed.

Only for someone developing some tools in the workflow.

hariszaf commented 1 year ago

So do we keep the tabix or remove it from the dependencies?

hariszaf commented 1 year ago

@jprmachado Stelios made a few changes and integrated the DEPENDENCIES file on the README so we keep the min number of files.

I merge this branch so we release and please feel free to edit and we add edits at any later point.