search

FredHutch / easybuild-life-sciences

Howto and implementation documentation
https://fredhutch.github.io/easybuild-life-sciences/
21 stars 6 forks source link

BALDR module install request #517

Closed moduff closed 2 years ago

moduff commented 2 years ago

I'm interested in running the BALDR pipeline (https://github.com/BosingerLab/BALDR) on a cluster. I have a lot of sequences to be analyzed, and it may be useful for others to have this installed as a module. If not, I'll pursue the other installation alternatives that are suggested here, thanks.

fizwit commented 2 years ago

The dependencies for BALDR are more than 5 years old. It could be an issue trying to build something that old with newer compilers. All the dependencies for BALDR are available on the cluster; IgBLAST, Trinity, Trimmomatic etc.. BALDR looks like a Perl wrapper for these tools? Maybe someone in SR or the bioinformatics group could suggest a newer pipeline.

('Trinity', '2.12.0'), # v2.3.2 (Newer versions are not compatible)
('IgBLAST', 'v1.6.1 (Newer versions are not compatible)
moduff commented 2 years ago

Thanks. It's ugly but still SOTA. I'll think about re-writing the Perl wrapper to work with current versions of the dependencies.

fizwit commented 2 years ago

way too many C compile errors using GCC 10 with Trinity 2.3.2. I tried

moduff commented 2 years ago

Would working with the Docker image avoid these issues? (I'm not an experienced Docker user, trying some things out on my desktop now.)