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/>

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