Here we go changeset: 8796:961ae35ba612 branch: stable tag: tip parent: 8794:1c7174911392 user: Nate Coraor <n...@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 <n...@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 <d...@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. >> >> 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 >> <mailto:bjoern.gruen...@googlemail.com> <bjoern.gruen...@gmail.com >> >> <mailto: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 >> <mailto: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 >> <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/ >> >> >> >> >> >> -- >> 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 >> > -- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865
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