I have problems understanding how environment variables are used/modified in galaxy.
I have some tools like, for instance, bedtools installed in /usr/local/bin which is in the path on a cluster and I would like this binary to be used. Some tools that launch bedtools after a pipe (i.e. ... | bedtools genomecov) do not find it. Another example was the special case of samtools where I found that linking the 0.1.19 version to a directory named default solved my problems.
So how can I tell galaxy tools to look first or always in /usr/local/bin? How can I check which instance (or version) of a software is being used?
Thanks for your help!