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





    ___________________________________________________________
    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:
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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

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 <nate@bx.psu.edu mailto:nate@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 <nate@bx.psu.edu mailto:nate@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 <dave@bx.psu.edu mailto:dave@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.gruening@googlemail.com
    <mailto:bjoern.gruening@googlemail.com>
    <mailto:bjoern.gruening@__googlemail.com
    <mailto:bjoern.gruening@googlemail.com>>
    <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>

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

    <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






    _____________________________________________________________
             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/

             To search Galaxy mailing lists use the unified search at:
    http://galaxyproject.org/__search/mailinglists/
    <http://galaxyproject.org/search/mailinglists/>





    --
    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