Re: [galaxy-dev] Error installing tools from toolshed

Fri, 20 Nov 2015 09:32:19 -0800 

Hi Scott,
can you try to update Trimmomatic (i.e. go to "Admin" -> "Manage installed tools" and click on "Install latest revision" on Trimmomatic menu) ? If this does not work, copy the relevant log from the Galaxy server and post it on the mailing list. 

Cheers,
Nicola

On 20/11/15 17:23, Scott Szakonyi wrote:

I was able to switch over to GitHub without issue. Thanks for pointing 
me in the right direction.



I have installed Trimmomatic successfully, although I wasn't able to 
install the latest version. If I try to install the "2015-09-23" 
revision, I get "Internal Server Error Galaxy was unable to 
successfully complete your request". The "2015-04-22" revision 
installs without issue.



I'm still having troubles with Picard as well, but one thing at a 
time! What information can I provide that might help with getting the 
latest issue of Trimmomatic?


Thanks!


On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo <nsora...@tiscali.it 
<mailto:nsora...@tiscali.it>> wrote:


    Hi Scott,
    the mercurial mirror is not up to date unfortunately, see this
    previous discussion:

    
http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html

    Cheers,
    Nicola


    On 20/11/15 13:13, Scott Szakonyi wrote:

    Hi Nicola,

    I'm not entirely sure which version... but I am still using the
    mercurial mirror, which says I'm up to date. Would this be a wise
    time, then, to change over to the Git repository directly?

    Thanks!

    Scott

    On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo
    <nsora...@tiscali.it <mailto:nsora...@tiscali.it>> wrote:

        Hi Scott,
        which Galaxy release are you using?
        This is a bug which should be fixed in an updated
        release_15.07 git branch.

        Cheers,
        Nicola

        ---- Scott Szakonyi ha scritto ----


        Hello all,

        I'm having issues installing Trimmomatic and Picard tools
        from the toolshed. The errors are of the following form
        (Trimmomatic used for the example).

        Trimmomatic 0.32 package shows an installation error.

        Error details:
        File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 142, in install_and_build_package_via_fabric
            tool_dependency = self.install_and_build_package( 
tool_shed_repository, tool_dependency, actions_dict )
          File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 136, in install_and_build_package
            dir = tmp_dir
          File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
            self.gen.throw(type, value, traceback)
          File 
"/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py",
 line 142, in _setenv
            yield
          File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 100, in install_and_build_package
            initial_download=True )
          File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py",
 line 32, in execute_step
            initial_download=initial_download )
          File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 685, in execute_step
            dir = self.url_download( work_dir, downloaded_filename, url, 
extract=True, checksums=checksums )
          File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 223, in url_download
            extraction_path = archive.extract( install_dir )
          File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py",
 line 89, in extract
            os.chmod( absolute_filepath, unix_permissions )

        [Errno 2] No such file or directory: 
'/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/'

        I've tried several version of the tool with no success. Any
        thoughts? I've searched project website but haven't come up
        with anything definitive.

        Thanks for any help you can offer,


        -- 
        Scott B. Szakonyi

        Research Programmer
        *Center for Research Computing*
        107 Information Technology Center
        Notre Dame, IN 46556
        <http://crc.nd.edu/>http://crc.nd.edu





    -- 
    Scott B. Szakonyi

    Research Programmer

    *Center for Research Computing*
    107 Information Technology Center
    Notre Dame, IN 46556
    <http://crc.nd.edu/>http://crc.nd.edu





--
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu <http://crc.nd.edu/>


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