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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Graham,

I was able to reproduce the error by updating to changeset 11216:c458a0fe1ba8, and I've determined that the bug causing this error was fixed in 11310:9bde6f2b9c59. I would recommend updating to the current stable release as described on the following page:

https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date

The news brief for the current release can be found at:

https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10

--Dave B.

On 02/12/2014 08:50 AM, graham etherington (TSL) wrote:

Hi Dave, Thanks for the prompt reply. Here’s the information that you asked for, plus some other bits and bobs.

$ hg summary parent: 11216:c458a0fe1ba8 Merge security fix for filtering tools from stable/next-stable. branch: default commit: 9 modified, 193 unknown update: (current)

$ python Python 2.6.6 (r266:84292, Nov 22 2013, 12:16:22) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2

Cheers, Graham

Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

From: Dave Bouvier <dave@bx.psu.edu mailto:dave@bx.psu.edu> Date: Wednesday, 12 February 2014 13:44 To: "graham etherington (TSL)" <graham.etherington@sainsbury-laboratory.ac.uk mailto:graham.etherington@sainsbury-laboratory.ac.uk>, Galaxy Dev <galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Error installing VarScan from Toolshed

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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