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:
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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