Closed jprmachado closed 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!
@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!
@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.
So do we keep the tabix or remove it from the dependencies?
@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.
Aim to improve the instructions to install and run the worflow
Open for discussion and help