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/__... <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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