SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
89 stars 29 forks source link

Bug with checking dependencies #20

Closed tseemann closed 4 years ago

tseemann commented 4 years ago
$diamond_bin = "diamond blastp" if `command -v diamond makedb;`;
command -v diamond makedb
/home/linuxbrew/.linuxbrew/bin/diamond
/home/linuxbrew/.linuxbrew/bin/makedb  # this is some other GNU tool

might have to do

iamond help | grep makedb
makedb  Build DIAMOND database from a FASTA file
SionBayliss commented 4 years ago

The same hold for testing diamond blastp (it find blastp):

command -v diamond blastp
/home/sbayliss/miniconda3/envs/PIRATE/bin/diamond
/home/sbayliss/miniconda3/envs/PIRATE/bin/blastp

I have changed it to just just search for diamond on cdmem. It will be pushed to master shortly.