Alex,

It is likely that the error you're encountering may have been resolved in the current stable branch. A description of the steps required to update your installation can be found on the following page:


https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date

Be advised that there is at least one database upgrade between the 2013-02-08 release and the current stable branch, so the paragraph describing database migration does apply.

Additionally, a number of tools were migrated to the tool shed from the Galaxy distribution since that release. A detailed explanation of this process and instructions for installing the repositories containing migrated tools can be found at the following page:

https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution

   --Dave B.

On 01/31/2014 09:14 AM, Alexander Kurze wrote:
Here we go

changeset:   8796:961ae35ba612
branch:      stable
tag:         tip
parent:      8794:1c7174911392
user:        Nate Coraor <n...@bx.psu.edu <mailto:n...@bx.psu.edu>>
date:        Fri Feb 08 11:23:04 2013 -0500
summary:     Added tag release_2013.02.08 for changeset 1c7174911392

changeset:   8795:9fd7fe0c5712
parent:      8785:25bd9d387135
parent:      8794:1c7174911392
user:        Nate Coraor <n...@bx.psu.edu <mailto:n...@bx.psu.edu>>
date:        Fri Feb 08 11:22:54 2013 -0500
summary:     merge from stable


961ae35ba612+ (stable) tip


Alex


On Fri, Jan 31, 2014 at 2:09 PM, Dave Bouvier <d...@bx.psu.edu
<mailto:d...@bx.psu.edu>> wrote:

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

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

             Hi Alex,

             there is a difference in
        http://toolshed.g2.bx.psu.edu/__view/devteam/package_bowtie2___2_1_0
        <http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0>
        and
        http://toolshed.g2.bx.psu.edu/__view/devteam/bowtie_wrappers
        <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
        <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.ku...@bioch.ox.ac.__uk
        <mailto:alexander.ku...@bioch.ox.ac.uk>
             <mailto:alexander.kurze@bioch.__ox.ac.uk
        <mailto:alexander.ku...@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>

        
<http://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 <tel:%2B44%201865%20613%20230>
        Fax:+44 1865 613 341 <tel:%2B44%201865%20613%20341>




--
Alexander Kurze
70 Sunningwell Road
Oxford, OX1 4SX

Tel:   +44 1865-243-609
Mobile:  +44 7962-425-865
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