Hi Scott, the mercurial mirror is not up to date unfortunately, see this previous discussion:
http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td...
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 mailto: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 <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/
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 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-td...
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/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
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 <nsoranzo@tiscali.it mailto: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 <mailto: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/>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/
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...." "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...." "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...." "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 nsoranzo@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 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-td...
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 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/ http://crc.nd.eduhttp://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/
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...." "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...." "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...." "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 <nsoranzo@tiscali.it mailto:nsoranzo@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 <nsoranzo@tiscali.it <mailto: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 <mailto: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/>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 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/
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 nsoranzo@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...." "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...." "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...." "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 nsoranzo@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 < nsoranzo@tiscali.it 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-td...
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 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/ http://crc.nd.eduhttp://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.eduhttp://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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-- 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/
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Scott Szakonyi