perl version 5.18.1 repository error
Dear all, i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9 Is this an error of my local instance or is the revision missing on the toolshed? Thank you very much for your help. Cheers, philipp
Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then select it again and "Install" it. Cheers, Nicola On 23/03/16 08:06, Rathert, Philipp, Dr. wrote:
perl version 5.18.1 repository error
Dear all,
i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.
however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies:
Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9
Is this an error of my local instance or is the revision missing on the toolshed?
Thank you very much for your help.
Cheers,
philipp
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Hi Nicola, Now I get this: <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?repository_id=c5770bc5f3721970&operation=browse&tool_dependency_ids=96aaea51084561ca> perl 5.18.1 package Error File "lib/tool_shed/galaxy_install/install_manager.py", line 123, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "lib/tool_shed/galaxy_install/install_manager.py", line 108, in install_and_build_package initial_download=False ) File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 1881, in execute_step job_name=package_name ) File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 118, in handle_command self.log_results( cmd, output, os.path.join( self.install_dir, basic_util.INSTALLATION_LOG ) ) File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 250, in log_results logfile = open( file_path, 'wb' ) [Errno 2] No such file or directory: u'/galaxy-central/tool_deps/perl/5.18.1/iuc/package_perl_5_18/d905bb415eca/INSTALLATION.log' From: Nicola Soranzo [mailto:nicola.soranzo@gmail.com] On Behalf Of Nicola Soranzo Sent: Mittwoch, 23. März 2016 12:49 To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] perl version 5.18.1 repository error Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then select it again and "Install" it. Cheers, Nicola On 23/03/16 08:06, Rathert, Philipp, Dr. wrote: Dear all, i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9 Is this an error of my local instance or is the revision missing on the toolshed? Thank you very much for your help. Cheers, philipp ___________________________________________________________ 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/
participants (3)
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Nicola Soranzo -
Philipp Rathert -
Rathert, Philipp, Dr.