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(a)nd.edu <mailto: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(a)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... 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(a)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/> -- 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/>