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(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/>