All tools need to be in the path of the user running galaxy.
Thon de Boer, Ph.D
T: +1.650.799.6839 | E-mail: thondeb...@me.com
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On Jan 21, 2012, at 3:50 PM, Andrew Warren <anwar...@vbi.vt.edu> wrote:
> 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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