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. Thanks, Chris Chris Cole wrote:
Hi all,
I'm trying install some local tools, but only locally to the galaxy user (e.g. ~/local_tools/bin). In order to avoid specifying the full path in each and every tool's XML file how can I specify a PATH for galaxy to find the binaries? It seems that Galaxy ignores the default $PATH although SGE can. Cheers,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev