Flag could not be matched: temp-dir about pggb HOT 3 CLOSED

Hi @Yutang-ETH,

regarding the first 3 points:

1. pggb on conda is less updated with respect to the github/docker/singularity ways. If you can, I would suggest these ways for the installation.
2. as your contigs are already partitioned by chromosome, I would suggest keeping them separated and running pggb on each chromosome separately and squeeze the graphs later (with odgi squeeze for example). This would make each run easier. You might evaluate later if run again pggb with everything together (we usually do this with smaller genomes).
3. it seems there is a version mismatch. conda-pggb still not fully support the -D\--temp-dir parameter. Again, using the github/docker/singularity ways would be better. When pggb is finalized (soon), we will make sure to keep the conda-way well updated as well.

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Hi @AndreaGuarracino

Thank you very much for your quick reply. I will try what you suggest and come back to report.

Best wishes,
Yutang

from pggb.

Hi @AndreaGuarracino

Please forgive me! I downloaded the latest release of pggb and now it works fine! Maybe add one option in pggb for version check?

Best wishes,
Yutang

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