search

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
203 stars 42 forks source link

Errors in env_setup.sh #86

Closed yumyai closed 1 year ago

yumyai commented 3 years ago

Hi,

I tried to install metagem on my server and found two problems.

  1. env_setup.sh tries to install GTBK's database at line 67, but it cannot find "download-db.sh` (https://github.com/franciscozorrilla/metaGEM/blob/master/env_setup.sh#L67).

  2. prokkaroary_env.yml has dependency conflict. It reports libzlib-1.2.11-h36c2ea0_1013 has constraint zlib 1.2.11 *_1013 conflicting with zlib-1.2.11-h516909a_1010 when I tried to create an environment it. It can be fix by bump up the version (https://github.com/franciscozorrilla/metaGEM/blob/master/envs/prokkaroary_env.yml#L331) to zlib=1.2.11=h36c2ea0_1013.

Best wishes, Preecha.

franciscozorrilla commented 3 years ago

Hi Preecha,

Thank you for brining this to my attention, this should now be fixed in the latest commit. I suspect that the manual installation is perhaps easier/more flexible than going through the script.

I am also thinking of simplifying/restructuring the env_setup.sh script to only set up the main metagem env during initial setup. I imagine that most users won't even use the prokka/roary tools, so I will make it a bonus feature rather than installing at the start. If you really want to use those tools, I would recommend to just conda install them manually in a separate environment.

Please let me know if you run into any other issues!

Best, Francisco