Hi Scott,
please always reply to the mailing list, because I may not be able to solve your issues.

I was able to install the latest revision of Trimmomatic without issues, so we may need some more information from the Galaxy logs to understand what is your issue.
Same for the other repositories.

Cheers,
Nicola

On 20/11/15 16:09, Scott Szakonyi wrote:
Hi Nicola,

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.

However, I'm still having problems with the Picard tool. I've tried sever of the revisions, and have similar issues with all. Dependencies are not installing correctly, and I'm unable to repair them or otherwise resolve the problem. Three of the tools that install with Picard end up missing dependencies: package_cairo_1_12_14, package_pixman_0_32_4, and package_readline_6_2. The underlying errors do not seem to have a definite pattern, as was the case when I was having problems before the GitHub switch. Is this something that I should take up with whoever provides the Picard tool?

Thanks!

Scott

On Fri, Nov 20, 2015 at 9:39 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu> wrote:
Hi Nicola,

Thank you, that's very helpful. I'll switch over to the GitHub repository and get the latest revision, then we'll see if that doesn't solve the problem.

Best,

Scott

On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo <nsoranzo@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 <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




--
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