Thanks Ross, the -v option is definitely a good way to go that I had
not considered. For anyone else following this thread, the tool
dependency environment system was just commented on and documented by
Nate.

See the following links:
http://galaxy-development-list-archive.2308389.n4.nabble.com/Documentation-for-Galaxy-s-tool-dependency-environment-system-td4321481.html
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies

Thanks!
-Andrew


On Tue, Jan 24, 2012 at 8:27 PM, Ross <ross.laza...@gmail.com> wrote:
>
> Without knowing exactly what 'a cluster with a similar setup to
> CloudMan' really means, if you're using SGE, passing the galaxy
> process's path to the job is usually accomplished by setting the -V
> flag in sge_request
> eg on an ubuntu 11.10 machine with 'default' as the queue
> (vgalaxy)galaxy@iaas1:$ cat /var/lib/gridengine/default/common/sge_request
> # system wide defaults
> -V
> -cwd
>
> works for me.
>
>
>
> On Wed, Jan 25, 2012 at 12:12 PM, Andrew Warren <anwar...@vbi.vt.edu> wrote:
> > Thanks for the replies. One extra element I failed to properly describe is
> > that we are running on a cluster with a similar setup to CloudMan. This
> > means we have a galaxyTools/tools directory with folders for each tool, and
> > subfolders for each version with a "default" symlink to the version
> > currently in use. Each subfolder has a "env.sh" script which is added by the
> > dependency manager to the qsub script to be processed at runtime . I was
> > thinking that one of the benefits of using the "requirements" tag is that it
> > would/could allow for tool and version specific dependency chains. For
> > instance if a version of tophat only runs with a certain version of bowtie
> > but you want to make the newest beta version of bowtie also available to run
> > independently.
> >
> > Right now the (sort of problem) I am having is that in order for the
> > necessary PATH information to be transmitted to the compute nodes I have to
> > have bowtie and samtools listed as requirements in the tool wrapper. The
> > PATH variable of the galaxy user doesn't transmit to the compute nodes
> > (despite having it set before launching the main instance of galaxy). With
> > our current setup I have seen this with several different tools that call
> > other tools and so I am wondering if my cluster/cloud setup has gone wrong
> > somewhere. Is there a "right" way or place to specify the runtime PATH so
> > that it will be transmitted to the compute nodes? Just trying to figure this
> > out in terms of "best practices" since my current setup seems to require
> > modification of the default wrappers to transmit PATH information to the
> > compute nodes.
> >
> > Thanks again,
> > Andrew
> >
> > On Sun, Jan 22, 2012 at 8:00 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
> >>
> >>
> >>
> >> On 01/22/2012 01:41 AM, Anthonius deBoer wrote:
> >>>
> >>> All tools need to be in the path of the user running galaxy.
> >>>
> >>
> >> but can be simply added to the path by adding them to the 'run.sh' script
> >>
> >> Regards, Hans
> >>
> >>
> >>
> >>> 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
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> >>>>
> >>>>  http://lists.bx.psu.edu/
> >>>
> >>>
> >>> ___________________________________________________________
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> >>>   http://lists.bx.psu.edu/
> >
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >  http://lists.bx.psu.edu/
>
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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