Nicola,

Sorry for the delay... holidays here in the US. That worked perfectly...
thank you very much!

Best,

Scott

On Fri, Nov 20, 2015 at 1:59 PM, Nicola Soranzo <nsora...@tiscali.it> wrote:

> Hi Scott,
> you can try to reinstall it with: "Admin" -> "Manage installed tools",
> then click on "Advanced Search" on top, then click on "Deactivated or
> uninstalled" and click on "Activate or reinstall" on Trimmomatic menu.
>
> Cheers,
> Nicola
>
>
> On 20/11/15 18:07, Scott Szakonyi wrote:
>
> Hi Nicola,
>
> Certainly. On screen, I get a message that says "Revision *f8a9a5eaca8a* of
> repository *trimmomatic* owned by *pjbriggs* has already been installed."
>
> In the logs:
>
> 129.74.33.163 - - [20/Nov/2015:12:51:44 -0400] "GET
> /admin_toolshed/browse_repositories?status=error&message=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.
> HTTP/1.1" 200 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/install_latest_repository_revision?id=d071e794759ab192
> HTTP/1.1" 302 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error&message=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/browse_repositories?status=error&message=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.
> HTTP/1.1" 200 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error&message=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/browse_repositories?operation=install+latest+revision&id=d071e794759ab192
> HTTP/1.1" 302 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error&message=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
>
> I'm not 100% sure these are in order... I have multiple web handlers
> running and the requests get spread out between them. I've tried to order
> them as best I can.
>
> Thanks!
>
> Scott
>
> On Fri, Nov 20, 2015 at 12:31 PM, Nicola Soranzo <nsora...@tiscali.it>
> wrote:
>
>> 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>
>> 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>
>>> 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>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>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
>>
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>
>
> --
> 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
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
>


-- 
Scott B. Szakonyi
Research Programmer

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