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" version="1.5.0">
    <description>Find splice junctions using RNA-seq data</description>
    <version_command>tophat --version</version_command>
        <requirement type="package">tophat</requirement>
        <requirement type='package'>bowtie</requirement>
        <requirement type="package">samtools</requirement>

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
registration deadline...doh.

Andrew Warren

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