Running a new or uncached instance of the pipeline will fail using docker, singularity, and test profiles

[nebfield]

Users will temporarily be unable to run pgsc_calc in new environments using the docker, singularity, and test profiles. You might see error messages like:

Error response from daemon: Head "https://dockerhub.ebi.ac.uk/v2/gdp-public/pgscatalog_utils/pgscatalog_utils/manifests/dev": received unexpected HTTP status: 500 Internal Server Error

Unable to read script: ...  -- cause: https://gitlab.ebi.ac.uk/nebfield/test-datasets/-/raw/master/pgsc_calc/samplesheet.csv

The server that hosts our container registry and test data is currently down for maintenance, and service will probably be intermittent until the start of next week.

If you've already ran pgsc_calc before, you can work around the problem by checking for previously reference downloaded data:

find work/ -name 'pgsc_calc_ref.sqlar'

And add a new parameter to your run:

--ref <path/to/pgsc_calc_ref.sqlar>

See #66 for more context.

[nebfield]

If you haven't used pgsc_calc before and would like to test the pipeline with the conda profile, please download and unzip:

pgsc_calc_ref.sqlar.zip

And manually set the --ref parameter to the path of the unzipped file.

[nebfield]

The gitlab server was fixed this morning (February 13, 2023). Sorry for the inconvenience!