Troubleshooting

Running Interactively on UKBiobank RAP

To debug errors, it may be useful to run the code interactively, for this, you can use the Cloud Workstation. This tutorial may also be useful. To start an instance:

dx run \
  --instance-type mem2_ssd1_v2_x8 \
  -imax_session_length="10h" \
  -y \
  --ssh app-cloud_workstation

To import one or multiple files (typically input files for a failed step):

dx download FILE_ID_1 FILE_ID_2...

Then you can download the docker image and enter a container:

docker run -it --rm -v $PWD:/mnt/data olivierlabayle/wdl-gwas:main /bin/bash

The current directory is mounted to /mnt/data. From there, work as usual, for instance to start a Julia REPL:

julia --project=/opt/PopGen --sysimage=/opt/PopGen/sysimage.so --startup-file=no

You can upload generated data to your project with dx upload:

dx upload --path "$DX_PROJECT_CONTEXT_ID:" <FILE>

Finally, when you are finished, terminate the job with the appropriate job-id:

dx terminate job-J1V4870JpYQP94jgb33y45qP