search

AuReMe / mpwt

Pathway Tools multiprocessing wrapper (for PathoLogic).
GNU Lesser General Public License v3.0
12 stars 0 forks source link

bypass the genetic-elements.dat and organisms.dat creation #79

Closed lcottret closed 11 months ago

lcottret commented 1 year ago

Hi !

I'm ready to use mpwt :-). In my pipeline, I generated all the genetic-elements.dat and organism.dat. Is there a way in mpwt to bypass the creation of these files if they are present in the input folders ?

Ludo

lcottret commented 1 year ago

To be more concrete, I put information in organisms.dat that I can't deal with in mpwt. For instance, the name of the species that I want to display (e.g to add the strain), the copyright, etc...

ArnaudBelcour commented 1 year ago

Hi @lcottret,

In the current version (0.7.2) mpwt will rewrite the input files, so it is not possible.

But I have made changes in the branch mpwt 0.8.0, that should keep the input files provided and not rewrite them.

Can you test it? A little warning: the version on the branch 0.8.0 is still in development, so I recommend to make copies of your file before testing it.

lcottret commented 1 year ago

Hi !

Thanks @ArnaudBelcour !

What is the easiest way to test the 0.8.0 version ? Is it possible to use pip ?

ArnaudBelcour commented 1 year ago

Hi,

I think the easiest way is to combine git and pip.

First, uninstall older version of mpwt with a pip uninstall mpwt.

Then clone the repository:

git clone https://github.com/AuReMe/mpwt.git

Move to the branch 0.8.0:

cd mpwt git checkout mpwt_0.8.0

Then install it with pip: pip install .

You can also add the -e (editable) option: pip install -e . With the -e option, pip will track the changes made on the git repository allowing to easily update to the new commits (in combination with git pull).