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 "" 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,

On Sun, Jan 22, 2012 at 8:00 AM, Hans-Rudolf Hotz <> 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 '' script

Regards, Hans



Thon de Boer, Ph.D
Bioinformatics Guru

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On Jan 21, 2012, at 3:50 PM, Andrew Warren<>  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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