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: thondeb...@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 <anwar...@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/

___________________________________________________________
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/

Reply via email to