All tools need to be in the path of the user running galaxy.
Regards,
Thon
Thon de Boer, Ph.D
Bioinformatics Guru
T: +1.650.799.6839 | E-mail: thondeboer(a)me.com
http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b
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On Jan 21, 2012, at 3:50 PM, Andrew Warren <anwarren(a)vbi.vt.edu> wrote:
Hello,
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>
<requirements>
<requirement type="package">tophat</requirement>
<requirement type='package'>bowtie</requirement>
<requirement type="package">samtools</requirement>
</requirements>
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.
Thanks,
Andrew Warren
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