Re: [galaxy-dev] software installs: PATH vs env.sh
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
"IMPORTANT NOTICE: This email message is legally privileged, confidential and is for
the use of the individual or entity to whom it is addressed. If you have received this
email message by error, please immediately notify us by email and delete the message.
Thank you."
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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/