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MRCIEU / opengwas-reports

Report module for IEU GWAS pipeline
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Deployment #6

Closed explodecomputer closed 5 years ago

explodecomputer commented 5 years ago

Hi @YiLiu6240

Could you please setup deployment such that the report module is running in a docker container similar to here:

https://github.com/MRCIEU/gwas_processing

So when the container is run you are mounting a volume that contains the data, and you can use docker exec to run the command from the host. Let me know if any issues

YiLiu6240 commented 5 years ago

Hi @explodecomputer I have added containerisation and could you give it a try?

As an example (using docker-compose):

git clone https://github.com/MRCIEU/mrbase-report-module mrbase-report-module
cd mrbase-report-module; git checkout docker
mkdir -p gwas-files/${ID} ref_data
cp path/to/${ID}/data{.bcf,bcf.csi} gwas-files/${ID}/
cp path/to/1kg_v3_nomult.bcf ref_data/  # or other reference data

docker-compose up -d
# The --refdata part is optional if refdata is ref_data/1kg_v3_nomult.bcf
docker exec mrbase-report render_gwas_report.R gwas-files/${ID}/data.bcf --refdata ref_data/1kg_v3_nomult.bcf

I have updated repo README for local usage and using vanilla docker. Let me know if there are any issues.

YiLiu6240 commented 5 years ago

@ValeriiaH for reference if you would like to play with the code, consult the example above and modify with the following

ValeriiaH commented 5 years ago

Thanks, @YiLiu6240. I'll try this, although I need to apply for the BC4 account first.

YiLiu6240 commented 5 years ago

@ValeriiaH You can use these files on epi-franklin

YiLiu6240 commented 5 years ago

Hi @explodecomputer, I added a branch "bcf-merge" that has your changes on the container structure and the changes that were ahead of master:

Please give this branch a try and if there is no problem you can rebase/merge bcf-merge onto master.

explodecomputer commented 5 years ago

@YiLiu6240 works great thanks for all your efforts on this!!