TaxCheck and last release

[tbazilegith]

Hi Azat, Does the last release (2022-12-13) of pgap support the flag --taxcheck-only ?

I ran this command (in python) for sample_id in pgdirlist: subprocess.run('${PGAP_INPUT_DIR}pgap.py -n --no-internet --ignore-all-errors --container-path ${PGAP_INPUT_DIR}pgap_20-22-12-13.build6494.sif --taxcheck-only -o ' + sample_id+'_taxCheck '+ pg_dir +'/'+ sampleid+'/input'+ sample_id + '.yaml --docker singularity', shell = True, check = True)

I encountered this error Exception: installation of some or all of components failed. Please remove /pgap//input-2022-12-13.build6494, pgap//test_genomes, /pgap//test_genomes-2022-12-13.build6494 directories and try again.

• This raised another question, (about the installation of pgap): Should we create the path variable PGAP_INPUT_DIR before downloading the file (wget https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py) of after?

• Imagined that why the installation of some components has failed...

Thanks, TJ

[tbazilegith]

I noticed that issue was addressed through issue #183 Thanks!

[azat-badretdin]

Thank you for your report, Tassy! Many apologies for not replying earlier.

Please let us know if this fixes your problem now