/ga4gh_NeSI

Primary LanguageShell

Deprecation notice- ga4gh-server is deprecated. Please refer https://github.com/ga4gh/htsget-refserver which is the new implementation

ga4gh_NeSI

  • To build docker & singularity, use ./build
  • To start singularity image, first do export REGISTRY_PATH=/wherever/something and then ./run_ga4gh
  • MAKE SURE that the registry folder is initialized (has at least registry.db)

To run on the cluster:

  1. choose a unique port that is not used by somebody else, high port numbers are probably safe, e.g. > 10000, here we use 10083, replace it with your chosen port in the commands below
  2. set up port forwarding, e.g. on your local machine run ssh -L 10083:localhost:10083 mahuika
  3. edit the Slurm script run_ga4gh_slurm (on the cluster)
    • set the environment variables
    • make sure to set GA4GH_PORT to the port you chose above
    • set the resource requirements (memory, wall time, etc)
  4. submit the run script to the queue sbatch run_ga4gh_slurm (on the cluster)
  5. check the status of the Slurm job squeue -u $USER (on the cluster)
  6. once the job is running, on your local machine connect to http://localhost:10083/