Singularity and panEDTA

[joannarifkin]

Hi there,

Thanks for developing EDTA - it's great! And I'm excited to run panEDTA - I've already successfully run EDTA on 10 related species.

Apologies if this is a silly question, but I'm having trouble figuring out the interface of panEDTA and the EDTA singularity container. I run EDTA from the singularity container (singularity exec ~/EDTA.sif EDTA.pl), but I can't figure out where in the container to execute panEDTA from, and when I execute the panEDTA script from outside the container, it cannot find EDTA.pl:

Can't open perl script "~/util/count_base.pl": No such file or directory Can't open perl script "~/EDTA.pl": No such file or directory ERROR: Initial EDTA failed for Ler.test.fa

I tried re-downloading panEDTA.sh into the singularity EDTA directory from within the singularity shell, but it said it was a read-only file system. What am I missing?

Thanks again!

Joanna