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 < 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>:
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 )
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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