Re: [galaxy-dev] Trinity installation
Hi Jose, can you please open an issue about this at https://github.com/galaxyproject/tools-iuc/issues/new ? Thanks for reporting the problem! Nicola On 10/06/16 12:33, Jose Juan Almagro Armenteros wrote: Hi again, I have been able to solve this problems thanks to fix commited by nsoranzo and I installed the package_trinity_2_1_1 correclty. However, when installing trinity (e4a9e0798360) there is a problem with the edger and express dependencies. In the trinity's tool_dependencies.xml file these two packages appear as: However, in the tool_dependencies.xml file from these packages they appear with a different name: Therefore, I suppose that Galaxy does not recognize them and they are shown as Never Installed. Could you look into this? Regards, Jose 2016-06-09 17:09 GMT+02:00 Jose Juan Almagro Armenteros : Hello, I am having troubles installing the last version of the tool Trinity. I found that I have the same error as this issue ( https://github.com/galaxyproject/galaxy/issues/1947), so I tried the suggested solution. It didn't work, so I posted the error in the issue. Then, I tried to change the tmp folder to another one in the same filesytem (and undoing the previous solution). Again it didn't work, but it gave a different error: File "/steno-internal/projects/galaxy/galaxy-dist/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 "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 108, in install_and_build_package initial_download=False ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 845, in execute_step destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 864, in move_directory_files shutil.move( source_file, destination_file ) File "/usr/lib/python2.7/shutil.py", line 130, in copy2 copyfile(src, dst) File "/usr/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: [Errno 21] Is a directory: '/steno-internal/projects/galaxy/galaxy-dist/tmp/tmp-toolshed-mtd8Exq2w/trinityrnaseq-2.1.1/trinity-plugins/jellyfish' I am using the Galaxy release *16.01. *Do you know how could I solve this problem? ___ 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/ ___ 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/
Re: [galaxy-dev] Trinity installation
Hi again, I have been able to solve this problems thanks to fix commited by nsoranzo and I installed the package_trinity_2_1_1 correclty. However, when installing trinity (e4a9e0798360) there is a problem with the edger and express dependencies. In the trinity's tool_dependencies.xml file these two packages appear as: However, in the tool_dependencies.xml file from these packages they appear with a different name: Therefore, I suppose that Galaxy does not recognize them and they are shown as Never Installed. Could you look into this? Regards, Jose 2016-06-09 17:09 GMT+02:00 Jose Juan Almagro Armenteros : > Hello, > > I am having troubles installing the last version of the tool Trinity. I > found that I have the same error as this issue ( > https://github.com/galaxyproject/galaxy/issues/1947), so I tried the > suggested solution. It didn't work, so I posted the error in the issue. > > Then, I tried to change the tmp folder to another one in the same > filesytem (and undoing the previous solution). Again it didn't work, but > it gave a different error: > > > File > "/steno-internal/projects/galaxy/galaxy-dist/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 > "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 108, in install_and_build_package > initial_download=False ) > > File > "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 31, in execute_step > initial_download=initial_download ) > > File > "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 845, in execute_step > > destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) > > File > "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 864, in move_directory_files > shutil.move( source_file, destination_file ) > File "/usr/lib/python2.7/shutil.py", line 130, in copy2 > copyfile(src, dst) > File "/usr/lib/python2.7/shutil.py", line 82, in copyfile > with open(src, 'rb') as fsrc: > > > [Errno 21] Is a directory: > '/steno-internal/projects/galaxy/galaxy-dist/tmp/tmp-toolshed-mtd8Exq2w/trinityrnaseq-2.1.1/trinity-plugins/jellyfish' > > I am using the Galaxy release *16.01. *Do you know how could I solve this > problem? > ___ 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/
[galaxy-dev] Trinity installation
Hello, I am having troubles installing the last version of the tool Trinity. I found that I have the same error as this issue ( https://github.com/galaxyproject/galaxy/issues/1947), so I tried the suggested solution. It didn't work, so I posted the error in the issue. Then, I tried to change the tmp folder to another one in the same filesytem (and undoing the previous solution). Again it didn't work, but it gave a different error: File "/steno-internal/projects/galaxy/galaxy-dist/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 "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 108, in install_and_build_package initial_download=False ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 845, in execute_step destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 864, in move_directory_files shutil.move( source_file, destination_file ) File "/usr/lib/python2.7/shutil.py", line 130, in copy2 copyfile(src, dst) File "/usr/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: [Errno 21] Is a directory: '/steno-internal/projects/galaxy/galaxy-dist/tmp/tmp-toolshed-mtd8Exq2w/trinityrnaseq-2.1.1/trinity-plugins/jellyfish' I am using the Galaxy release *16.01. *Do you know how could I solve this problem? ___ 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/
