I have written a simple xml wrapper to run the UCSC *bigWigToBedGraph* tool
on a custom Galaxy install on Amazon cloud. The tool works as expected in
this install. The xml file itself is in
/mnt/galaxy/galaxy-app/tools/myTools, but I added the bigWigToBedGraph
binary to the /mnt/galaxy/tools/bin/ directory, which is by default in the
PATH. Alternatively, I guess I could have modified the PATH so that it
includes the myTools directory.
Since I would like to contribute the tool (my contribution being the
wrapper) to *Galaxy Tool Shed*, I am wondering* what is the best way to
include it so that it is found in the PATH* whenever the tool is installed
from the Tool Shed.
Thanks for your help!