Chris Cole wrote:
Digging more deeply I see some inconsistency in how some of the tools are executed.
Given this definition in the tool's xml: <command>fastx_trimmer -v -f $first -l $last -o $output</command>
The following command is generated in the Galaxy script: fastx_trimmer -v -f 5 -l 21 -o /homes/www-galaxy/galaxy_live/database/files/000/dataset_187.dat
However, given this definition: <command interpreter="perl">collate.pl --in $input --out $out1 --rm-ambi $ambi --length $min --prefix $prefix</command>
This command is generated: perl /homes/www-galaxy/galaxy_live/tools/solexa/collate.pl --in /homes/www-galaxy/galaxy_live/database/files/000/dataset_97.dat etc...
Why does the perl type have a path prefixed to the command whereas the other one doesn't? Plus, where is that path defined as it's not one I've set?
Finally, and more generally, which paths does Galaxy search for finding tools, if not explicitly set?
I've had a look on the wiki, but I can't find this information. Any help would be appreciated.
Hi Chris,
As you've discovered, tools are expected to be located in the same directory as their xml file if an interpreter is set. If an interpreter isn't set, $PATH is used instead (but the interpreter itself is assumed to be on the $PATH). This allows tools to be installed independently of Galaxy, but for the wrapper scripts within Galaxy to still be locatable.
--nate