Question: Error installing package_snpeff_4_0
0
lanceparsons1 • 0 wrote:
When attempting to install `package_snpeff_4_0` I consistently run into the following error:
tool_shed.galaxy_install.install_manager ERROR 2015-08-31 17:17:22,140 Error installing tool dependency snpEff version 4.0.
Traceback (most recent call last):
File "/data/galaxy-dev/galaxy-dev/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 "/data/galaxy-dev/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package
initial_download=True )
File "/data/galaxy-dev/galaxy-dev/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step
initial_download=initial_download )
File "/data/galaxy-dev/galaxy-dev/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 "/data/galaxy-dev/galaxy-dev/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download
extraction_path = archive.extract( install_dir )
File "/data/galaxy-dev/galaxy-dev/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract
os.chmod( absolute_filepath, unix_permissions )
OSError: [Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdJGmVRg/snpEff/snpEff/'
I have tried repairing, uninstalling, reinstalling, etc. to no avail. I even updated to the not yet released realease_15.07. No dice. Ultimately, I'd like to get the CloudMap workflow running, which actually uses a version of those tools that are no longer available, so this seemed the best choice.
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modified 3.1 years ago
by
Bjoern Gruening ♦ 5.1k
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written
3.2 years ago by
lanceparsons1 • 0
