Question: Error installing package_snpeff_4_0
gravatar for lanceparsons1
2.6 years ago by
United States
lanceparsons10 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/", 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/", line 100, in install_and_build_package
    initial_download=True )
  File "/data/galaxy-dev/galaxy-dev/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 32, in execute_step
    initial_download=initial_download )
  File "/data/galaxy-dev/galaxy-dev/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", 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/", 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/", 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.

ADD COMMENTlink modified 2.5 years ago by Bjoern Gruening5.0k • written 2.6 years ago by lanceparsons10
gravatar for Bjoern Gruening
2.5 years ago by
Bjoern Gruening5.0k
Bjoern Gruening5.0k wrote:

I guess this was (hopefully not anymore) a problem with the uncompressing of archive with a strange directory hierarchy. As far as I know this is fixed. Can you confirm this?



ADD COMMENTlink written 2.5 years ago by Bjoern Gruening5.0k

Yes, this does appear to be fixed now. If I could remember the exact fix, I'd post it here. Any ideas? ;-)

ADD REPLYlink written 2.5 years ago by Lance Parsons110
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