Graham,

I've not been able to duplicate that error on my local instance, which is running the most recent revision on the stable branch. To help track down this issue, could you paste the output of 'hg summary' run from the Galaxy installation path?


   --Dave B.

On 02/12/2014 06:13 AM, graham etherington (TSL) wrote:
Hi,
I’m trying to install VarScan from the Main Toolshed. I’ve tried both
the versions available (‘varscan’ from fcaramia and ‘varscan_version_2’
from devteam), but I get the same error each time:

File
"/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py",
line 294, in install_and_build_package_via_fabric
fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
File
"/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py",
line 619, in install_and_build_package destination=full_path_to_dir )
File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
self.gen.throw(type, value, traceback)
File
"/tsl/services/galaxy/dist/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py",
line 142, in _setenv yield
File
"/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py",
line 309, in install_and_build_package dir =
td_common_util.url_download( work_dir, downloaded_filename, url,
extract=True )
File
"/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py",
line 434, in url_download archive = CompressedFile( file_path )
File
"/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py",
line 27, in __init__ self.type = self.file_type 'CompressedFile' object
has no attribute 'file_type'

Can anyone suggest what might be going wrong here?
Many thanks,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601


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