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
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