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precimed / gsa-mixer

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Discrepancies between GSA_MIXER.job and main page README #6

Open nievergeltlab opened 2 months ago

nievergeltlab commented 2 months ago

Hi,

On the readme page of this github, there are some example commands for running gsa-mixer

For --gsa-base, the input parameters include: --go-file go-file-baseline.csv \ --go-file-test go-file-geneset.csv

For --gsa-full the input parameters include: --go-file go-file-gene.csv \ --go-file-test go-file-geneset.csv

But is --go-file-test compatible with --gsa-base? I thought that you need to specify --load-params-file to use --go-file-test. The input json file for this parameter is an output of --gsa-base, thus would not be available for the base step.

In contrast to the README page, the file GSA_MIXER.job in the scripts directory does not have '--go-file-test' as a parameter when executing --gsa-base

Also in contrast to the README page, the file GSA_MIXER.job does not include the --extract command that is used to extract subsets of reference SNPs, nor does it include the array indexing of the multiple runs.

thanks!

humanpaingeneticslab commented 1 month ago

Greetings!

It seems that we're in the same trying-to-get-this-thing-work boat! :-)

Regarding the issue above, I was able to run the tutorial by removing this line: --go-file-test go-file-geneset.csv when calling '${MIXER_PY} plsa --gsa-base ...'

Now, I was wondering if you could get your hands on either UKB's or HRC's reference files, those listed in that section here: https://github.com/precimed/gsa-mixer?tab=readme-ov-file#download-ld-reference-files

Thanks!