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 <nsoranzo@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

--

Scott B. Szakonyi

Research Programmer

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