search

comorment / gwas

GNU General Public License v3.0
4 stars 1 forks source link

Make container with LD score regression #18

Closed ofrei closed 3 years ago

ofrei commented 4 years ago

I might need https://github.com/bulik/ldsc in a separate Docker container. https://hub.docker.com/r/manninglab/ldsc/dockerfile - could this be a starting point?

bayramakdeniz commented 4 years ago

this can be done with a separate container: https://github.com/bayramakdeniz/ldsc

ofrei commented 4 years ago

The ldsc.sif runs fine, but https://github.com/bayramakdeniz/ldsc doesn't have Dockerfile - could you please add it?\ Also, we'll need to organize reference data required for LD Score Regression. It's available here: https://alkesgroup.broadinstitute.org/LDSCORE but we don't need all of it. Some relevant data files are mentioned in here: https://github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation I've already worked with LDSC so I can help to select the files that are needed. Could you organize Dockerfile in a way that I suggested here https://github.com/comorment/gwas/issues/11 (i.e. to have a install_ldsc.sh script that is then used from within Dockerfile ?). I will then directly update install_ldsc.sh with all files that should came together with LDSC container.

bayramakdeniz commented 4 years ago

The Dockerfile for LDSC has been added. It includes 3 parts (some basic tools, miniconda and install_ldsc.sh)

ofrei commented 4 years ago

@bayramakdeniz Thanks! I'll test it out.

ofrei commented 3 years ago

I've tested it out and it works well. Let's discuss on Wednesday, I suggest to further clarify the readme files and provide usage examples.

ofrei commented 3 years ago

@bayramakdeniz Here is a fix for ldsc container: https://github.com/comorment/gwas/commit/686d972d25ced7ffecd83760a28cf303a7ff53a5 (following https://github.com/bulik/ldsc/issues/112#issuecomment-379690505 ). I think this ticket can be closed - ldsc container works well.

bayramakdeniz commented 3 years ago

Yes, I checked it too and it works without an issue. Many thanks