[BUG] PGAP fails on test genome when PGAP_INPUT_DIR set to other than default

[mdziurzynski]

[BUG] PGAP fails on test genome when PGAP_INPUT_DIR set to other than default

[azat-badretdin]

Thank you for your report, user @mdziurzynski

Upon examination of the cwltool.log file I concluded that somehow part of reference data is missing. I would recommend to repeat the installation step in Quick Start after cleanup in your .pgap directory as recommended and try again.

[azat-badretdin]

Did you manage to try to reinstall PGAP and run it successfully?

[mdziurzynski]

Yes, I had to install PGAP without changing the default PGAP_INPUT_DIR. Then it worked.

But just for the reference - I reinstalled multiple times (and redownloaded the data) with different PGAP_INPUT_DIR vars, and it did not work even once.

[azat-badretdin]

I reinstalled multiple times (and redownloaded the data) with different PGAP_INPUT_DIR vars, and it did not work even once.

Is it possible that the location of PGAP_INPUT_DIR was on the filesystem somehow inaccessible to Docker?

Feel free to open a separate ticket for one of the PGAP_INPUT_DIR settings? Information we are looking for is mount location of the working directory and PGAP_INPUT_DIR directory and the relationship of those mounts with docker settings