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opain / GenoPred

Genotype-based Prediction (GenoPred)
https://opain.github.io/GenoPred/
GNU General Public License v3.0
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Preparation resources #65

Closed AndreaConti0 closed 2 years ago

AndreaConti0 commented 2 years ago

Hi, I don't know if something in my analysis go wrong but I think that it could be simplier if you would introduce in the gz folder test_data/target/imputed_sample_bgen/ the index for every chromosome file (in my case the absence of these files cause a crash of the GenoPredPipe).

Another thing ... I think that you can specified in step 2 of the "getting starded" point, the installation of ghostscript package sudo apt-get update sudo apt-get ghostscript ... because someone could haven't it, but the R function bitmap() require the presence of ghostscript.

Maybe, I could be wrong, but in case I'm waiting for news.

opain commented 2 years ago

Hello,

Apologies, the requirement for .bgi files for bgen format is new and I have not been able to update the test_data yet due to very slow upload speeds to zenodo (I don't know why). Hopefully I will be able to make the upload in the next few days.

Thank you for highlighting the need for ghostscript. I will make a note of this in the README.

opain commented 2 years ago

This has now been resolved in the latest push.