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> > 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 >> >> >> > > > -- > 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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