hattivatti

hattivatti submits pgsc_calc jobs to Puhti HPC at CSC. Jobs are configured to execute in a secure way because genomes are sensitive data. hattivatti is a proof of concept for testing sensitive data submission to CSC.

Run hattivatti

See Releases for most recent stable versions of hattivatti. The development version can be run with:

$ git clone https://github.com/ebi-gdp/hattivatti.git --branch dev
$ cargo run

Documentation

$ cargo doc --open

Deployment notes

Puhti is currently on RHEL 7 with an old version of glibc.

Github actions builds with rust-buster to match glibc version (2.28).

Cronjob

cron shell doesn't load much:

$ # load 'module' command
$ source /appl/profile/zz-csc-env.sh

Set environment variables

Sensitive variables:

$ export AWS_ACCESS_KEY_ID=<...>
$ export AWS_SECRET_ACCESS_KEY=<...>
$ export CALLBACK_TOKEN=<...>

Configuration variables:

$ export RUST_LOG=info
$ export NXF_SINGULARITY_CACHEDIR=<path>

Configure globus-file-handler-cli

Download the jar and set path as a parameter (--globus-jar-path)

The spring config directory must be in the same directory as the jar with the name config/. The spring config contains secrets for the transfer.

Clone pgsc_calc

$ cd /scratch/projec_XXXXXX/
$ nextflow clone https://github.com/PGScatalog/pgsc_calc.git

Run hattivatti

$ hattivatti --schema-dir repo/data/schemas  --work-dir work --globus-jar-path globus.jar

Backup database (optional)

After hattivatti executes the database will have no connections.

$ module load allas
$ rclone copy work/hattivatti.db s3allas://bucket/hattivatti/hattivatti.db

Dependencies

• curl (callback)
• globus-file-handler-cli (data transfer)
• nextflow (pgsc_calc)
  • java 16 (nextflow and data transfer)
• parallel (data transfer)
• SLURM (submitting jobs)

Note: pgsc_calc is executed using the singularity profile. All bioinformatics software is automatically fetched from a container registry. Images are cached after first fetch.