Alex,

To help determine the cause of this, could you paste the output of the following commands run from the root of your Galaxy installation?

hg heads
hg id

   --Dave B.

On 01/31/2014 09:05 AM, Alexander Kurze wrote:

Thanks for your quick answers.

I actually have installed the dependencies first and then I have tried
to add bowtie2 http://toolshed.g2.bx.psu.edu/view/devteam/bowtie2.

But this is where the problem lies: I get following error message:


  "Server Error

An error occurred. See the error logs for more information. (Turn debug
on to display exception reports here)"


Meanwhile, I have downloaded the bowtie2.xml and added it to the
./tools/sr_mapping/ folder and added it to the tool_config.xml and it
now works.

Any clue why I get the error message? Is there something wrong with my
server or do is it the repository?

Cheers,

Alex


On Fri, Jan 31, 2014 at 1:18 PM, bjoern.gruening@googlemail.com

<mailto:bjoern.gruening@googlemail.com> <bjoern.gruening@gmail.com

<mailto:bjoern.gruening@gmail.com>> wrote:

    Hi Alex,

    there is a difference in
    http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and
    http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers
    The package_* is installing the binary for you and can be used by
    other programs as well. bowtie_wrappers contains the actual wrappers
    and is depending on package_*. To make it short. You need to install
    http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both
    packages will be installed and you should see your wrapper.

    Ciao,
    Bjoern


    2014-01-31 Alexander Kurze <alexander.kurze@bioch.ox.ac.uk

    <mailto:alexander.kurze@bioch.ox.ac.uk>>:

        Hi there,

        I have a local copy of galaxy and I am trying to install bowtie2
        2.1.0 onto the system via the toolshed. However it just doesn't
        work. I always get a Server Error message. I have checked if the
        dependencies are installed and they are all installed in the
        toolshed depenencies folders. However, the actual repos only
        contains the tool_dependency.xml. (eg
        galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml

        <http://testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml>)

        I thought that there should be a bowtie2.xml file in the repos
        of package_bowtie_2_1_0 but there isn't...

        Also, looking at the shed_tool_config.xml I cannot see any entry
        for bowtie2.

        Is there a way to add bowtie2 manually?

        Best wishes,

        Alex





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--
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United Kingdom

Tel: +44 1865 613 230
Fax:+44 1865 613 341