use parallel instead of xargs ?

[tseemann]

./scripts/run_PIRATE.pl:        `cat $pirate_dir/genome_list.txt | xargs -I {} cat $pirate_dir/genome_multifastas/{}.fasta > $pirate_dir/pan_sequences.fasta`;

I think this command just cats all the files in the list together into a single fasta?

Having issues in conda with -I {} . Can we use parallel -j1 somehow instead?

UPDATE: not sure if this is the real problem

[SionBayliss]

It does! I will update it in the next push. Doesn't seem to get in the was of conda atm.

[SionBayliss]

Just saw your PR. Much appreciated!