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 <d...@bx.psu.edu <mailto:d...@bx.psu.edu>>
Date: Wednesday, 12 February 2014 13:44
To: "graham etherington (TSL)"
<graham.ethering...@sainsbury-laboratory.ac.uk
<mailto:graham.ethering...@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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