splitfa installation

[downingtim]

Just FYI, you need to install a different splitfa from here: https://github.com/lh3/psmc/
Then add it to your PATH
And then pgge works. The linked splitfa does not work.

Also, "pggb_yeast/consensus.gfa" does not work. You need the correct gfa file extension.

[subwaystation]

Hi @downingtim,

can you please elaborate what the problem is with the current splitfa from https://github.com/ekg/splitfa?

There is no pggb_yeast/consensus.gfa file nor folder in this repository. What are you talking about?

[downingtim]

Hi, I am using a normal Ubuntu / Bash OS, but splitfa does not work for me. Not 100% sure why.

In relation to the gfa file, I think my quotes got removed. For me at least, the "pggb_yeast/consensus.gfa" file in the command below does not work, it needs to be the exact gfa file name:

./pgge -g "pggb_yeast/consensus.gfa" -f data/yeast/cerevisiae.pan.fa.gz -t 16 -r scripts/beehave.R -l 100000 -s 50000 -o pgge_yeast

[subwaystation]

I think you have to add the *.

./pgge -g "pggb_yeast/*consensus.gfa*" -f data/yeast/cerevisiae.pan.fa.gz -t 16 -r scripts/beehave.R -l 100000 -s 50000 -o pgge_yeast

[subwaystation]

Where are you stuck with splitfa? Did you open an issue at https://github.com/ekg/splitfa?

[subwaystation]

There is also a docker image available for PGGE. https://github.com/orgs/pangenome/packages/container/package/pgge.