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.gruen...@googlemail.com < 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 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.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 >> ) >> >> 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/ >> > > -- 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
___________________________________________________________ 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/
