[Transdecoder-users] Minor fix: ln: creating symbolic link `Trinity.fasta.transdecoder.pfam.dat.domtbl': File exists

[Joel F. M. <joe...@mc...>]

Hi Brian,

When I rerun transdecoder in a directory where it was already run, I get an error during symlink creation:
ln: creating symbolic link `Trinity.fasta.transdecoder.pfam.dat.domtbl': File exists

Not a big deal; I can delete the symlink first but maybe you could do it in the same way you overwrite other files.

I guess it's in:

trinityrnaseq_r20140413p1/trinity-plugins/TransDecoder_r20131110/pfam_runner.pl

lines 183 and 210: replace

&process_cmd("ln -s $pfam_out $pfam_out.domtbl");

by

&process_cmd("ln -s -f $pfam_out $pfam_out.domtbl");

Thanks for your work!
Best
Joël