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contributing.md

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Maintaining reference dataset

Reference dataset is maintained as a github repository here: https://github.com/norment/comorment_data Note that this repository has git lfs support enabled.

Installing Docker and Singularity

  • TBD: provide insturctions for Docker installation.

  • To install it on Ubuntu follow steps described here: https://sylabs.io/guides/3.7/user-guide/quick_start.html Note that sudo apt-get can give only a very old version of singularity, which isn't sufficient. Therefore it's best to build singularity locally. Note that singularity depends on GO, so it must be installed first.

Building everything

There is a Makefile script in the root of the repo. To build all containers, run sudo make (or just make - it might be that you Docker & singularity are installed in a way that don't require sudo). Makefile builds conatiner xxx only if it's xxx.sif file is missing, or is older that containers/xxx/Dockerfile. You may touch containers/xxx/Dockerfile if you want to force the build (e.g. in case if one of the install_xxx.sh files has changed in the scripts folder - such dependency won't be handled by the Makefile).

Building docker images

Clone from http://github.com/comorment/gwas. The following commands assume that current directory is at the root the gwas repository.

docker build -t hello -f containers/hello/Dockerfile .
docker build -t gwas  -f containers/gwas/Dockerfile .
docker build -t python3 -f containers/python3/Dockerfile .
docker build -t ldsc  -f containers/ldsc/Dockerfile .
docker build -t r     -f containers/R/Dockerfile .

Building singularity containers

The script works by creating a local Docker repostiory:

singularity/from_docker_image.sh hello
singularity/from_docker_image.sh gwas
singularity/from_docker_image.sh python3
singularity/from_docker_image.sh ldsc
singularity/from_docker_image.sh r

Running docker containers (misc commands)

docker run -it r
docker run -it -v $COMORMENT_REF:/ref demo

Running singularity containers (misc commands)

singularity shell --no-home -B $(pwd):/data demo.sif
singularity shell --no-home -B $(pwd):/data python3.sif

misc

Docker quickly consumes a lot of disc space. Use sudo docker system df to check current usage, and sudo docker system prune -a to clean up.

Issues with internet inside Docker containers

This was useful: https://stackoverflow.com/questions/20430371/my-docker-container-has-no-internet