UCSF Wynton alphafold prediction run_alphafold232.py should handle absolute fasta file paths

[Tom Goddard]

My Python script for running AlphaFold predictions on the UCSF Wynton cluster described here

https://www.rbvi.ucsf.edu/chimerax/data/singularity-apr2022/alphafold_wynton.html

fails if an absolute fasta file path is specified with a "File not found" error because the directory containing the fasta has not been made visible to the singularity image with a -B option. Only the current working directory is made visible. This has been a hard to debug problem for Mike Trnka and Kate Crawford.

I should add a -B option to handle absolute fasta paths and absolute output directory paths.

[Tom Goddard]

In fact singularity includes the user's home directory and the current working directory binding by default

​https://docs.sylabs.io/guides/3.1/user-guide/bind_paths_and_mounts.html

"In the default configuration, the system default bind points are $HOME , /sys:/sys , /proc:/proc, /tmp:/tmp, /var/tmp:/var/tmp, /etc/resolv.conf:/etc/resolv.conf, /etc/passwd:/etc/passwd, and $PWD."

So the failing cases are when the fasta file is not under the home directory or current directory or temp directories. I guess that is why I had not seen it before.

[Tom Goddard]

Done.

If the fasta path is absolute or the output directory path is absolute then I add the containing directories to the list of singularity accessible directories. Tested using chimerax nobackup directory outside my home directory and not in temp.