Catalog plots

Generate study table with summary stats true/false status

Local

1. Docker needs to be installed: https://docs.docker.com/get-docker/
2. Using a terminal run the following (cd to the directory you want the output to be written to):

• docker run -it ebispot/gwas-utils python /catalogPlots/gwas_cat_plus_ss.py

3. Let it run (it may take several minutes to collect all the data from the REST API
4. The output is written to the current working directory to a file called study_download_with_sumstats_status_YYYY-MM-DD.tsv

• Note If you need to update the docker container to reflect any changes in the software:
• docker pull ebispot/gwas-utils to pull the latest docker image

Compute cluster (LSF)

1. login to cluster and cd to the directory you want the output written to
2. bsub -M4000 -R "rusage[mem=4000]" "singularity exec docker://ebispot/gwas-utils:latest python /catalogPlots/gwas_cat_plus_ss.py"
3. wait for email from lsf to tell you it's done