We recently transitioned from a CloudMan instance of galaxy to our own
cluster and started having problems with calls to tools from within
other tools. For example when Tophat calls bowtie-inspect its not
finding the executable. To fix this I listed bowtie in the
requirements section of the tophat wrapper like so:
<tool id="tophat" name="Tophat for Illumina"
<description>Find splice junctions using RNA-seq data</description>
Now I am wondering, is it generally expected that all tools used by
galaxy will have their executables on the user galaxy's PATH? Is the
above a good solution? Or is there something else likely amiss with
our galaxy setup? I think we recently pulled updates for some major
tool_shed release but I haven't been able to determine if any of the
tools listed above were affected by that.
Wish I were in Český Krumlov asking this question. Missed the