Inquiry about dependencies about metabolic HOT 5 OPEN

Thanks, @patriciatran . I don't want to speak on behalf of an entire community of users but personally I think having a software + the dependencies downloadable using conda could be beneficial (perhaps easier) to a lot of users. In the end it depends on what the developers think is best of course :) In the meantime I'm happy to set up all dependencies manually and give METABOLIC a go. Looking forward to the paper. Good luck.

Thanks,
A

from metabolic.

Hi @Ahmed-Shibl ,

Thank you for your message! At the moment you need to download and set up the dependencies (R packages, Perl modules, and the dependencies listed here ) yourself first. Depending on if you want to run METABOLIC-C or G, then you dependencies requirements will differ (see what I wrote in parentheses "(only for METABOLIG-C)"). Then, you can clone the directory (that will contain all the databases and hmms, so you don't need to download those separately).

At the moment we don't have it set up to be downloadable using conda, we can definitely look into that option if that makes it easier for our users! The paper is not out yet, and yes it's only just available on biorxiv. As you can see we made many updates to the software since we put the BioRxiv preprint out, so our future submitted paper will be different from that.

Thanks and please let us know if you have any questions.

Best, Patricia

from metabolic.

A conda install would be great! I am having a lot of trouble installing all the dependencies.

Thanks,
Sarah

from metabolic.

Hi all, just to let you know that another user has posted some instructions for a successful conda install here: #27 . Please try it out if you wish and provide feedback!

from metabolic.

Hi,

I just wanted to chip in: for me the greatest bottleneck for using METABOLIC has been installing the dependencies.
I have tried now following Dan's instructions in this other thread but I get conflicting dependency versions between bamtools, sambamba and coverm...
I agree that a conda recipe would be really useful.

I am really looking forward to trying out METABOLIC, hope I will be able to some day :)

Cheers,

Igor

from metabolic.