Still getting fasttree error

[tseemann]

 - WARNING: PIRATE could not make binary tree (is fastree installed?)
 - WARNING: PIRATE could not make R plots (are dependencies installed?)

 - tests completed

 $ PIRATE --version
PIRATE 1.0.2

which FastTree
/home/linuxbrew/.linuxbrew/bin/FastTree

From #8

../scripts/run_PIRATE.pl:$ft = "FastTree" if `command -v FastTree;`;
../scripts/run_PIRATE.pl:$ft = "fasttree" if `command -v fasttree;`;

I think these both always return true.

I am preparing a PR.

[SionBayliss]

I seem to have both executables in my path after installing fasttree via conda. I tested the script by renaming one or the other and it seemed to correctly report and run the executable.

[tseemann]

You are right. I think i must have accidently been on a local shell not on my server.

for CMD in ls perl FastTree fasttree prokka; do perl -e '$x=$ARGV[0];$c=`command -v $x`;print($c?"$x EXISTS\n":"$x NOT_INSTALLED\n");' $CMD ; done
ls EXISTS
perl EXISTS
FastTree EXISTS
fasttree NOT_INSTALLED
prokka EXISTS