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
___________________________________________________________ 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/