fasttree vs FastTree still not working

[tseemann]

$ command -v fasttree

$ command -v FastTree
/home/linuxbrew/.linuxbrew/bin/FastTree

./PIRATE  --check

Running PIRATE on test files:

 - PIRATE completed with no errors

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

 - tests completed

Not sure what is happening here:

../scripts/check_dependencies.pl:# fasttree
../scripts/check_dependencies.pl:$ft = 1 if `command -v fasttree;`;
../scripts/check_dependencies.pl:$ft = 1 if `command -v FastTree;`;
../scripts/check_dependencies.pl:print " - WARNING: fasttree not found in system path, a binary presence-absence tree will not be created.\n" if $ft == 0;
../scripts/run_PIRATE.pl:# set fasttree executable
../scripts/run_PIRATE.pl:$ft = "FastTree" if `command -v FastTree;`;
../scripts/run_PIRATE.pl:$ft = "fasttree" if `command -v fasttree;`;
../scripts/run_PIRATE.pl:# create binary fasta file for fasttree
../scripts/run_PIRATE.pl:if (`command -v fasttree;`){

[SionBayliss]

The tree file is being created correctly. The files that it is expecting are being removed before they can be check by the wrapper script due to the test directory being recently changed to a temp directory created using tempdir(). I am looking into it.

[SionBayliss]

Fixed on cdmem and will be pushed to master shortly. PIRATE was not correctly referencing the temp directory.