Hi Lance,
You'll need to execute the following sql manually in your Galaxy database.
update tool_shed_repository set status = 'New' where status = 'Cloning';
Next, you'll have to update your production Galaxy instance code base to at least
changeset 2531e085f262 (the human-readable changeset revision is 7503). This revision is
required to install the freebayes tool from the main Galaxy tool shed. You can also
choose to wait until the next Galaxy release to upgrade if you do not need the freebayes
tool in your local instance immediately.
Sorry for the inconvenience on this.
Greg Von Kuster
On Aug 31, 2012, at 3:59 PM, Lance Parsons wrote:
Thanks for the explanation. That makes sense. I went ahead and
installed the new version along with dependencies in my development environments and all
went well. Then in production, the installation seems to have failed and I'm now
stuck with freebayes in the "cloning" status. I tried to deactivate and
uninstall it so I could try again to monitor what went wrong and I just get an error:
Error - <type 'exceptions.AttributeError'>: 'NoneType' object has
no attribute 'startswith'
URL:
http://galaxy.princeton.edu/admin_toolshed/browse_repositories?operation=...
File
'/data/local/galaxy/galaxy-prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/data/local/galaxy/galaxy-prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line
80 in __call__
return self.application(environ, start_response)
File
'/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
return self.app( environ, start_response )
File
'/data/local/galaxy/galaxy-prod/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/base.py', line 160
in __call__
body = method( trans, **kwargs )
File '/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/__init__.py', line
184 in decorator
return func( self, trans, *args, **kwargs )
File
'/data/local/galaxy/galaxy-prod/lib/galaxy/web/controllers/admin_toolshed.py',
line 356 in browse_repositories
return self.deactivate_or_uninstall_repository( trans, **kwd )
File '/data/local/galaxy/galaxy-prod/lib/galaxy/web/framework/__init__.py', line
184 in decorator
return func( self, trans, *args, **kwargs )
File
'/data/local/galaxy/galaxy-prod/lib/galaxy/web/controllers/admin_toolshed.py',
line 408 in deactivate_or_uninstall_repository
repository_install_dir = os.path.abspath ( relative_install_dir )
File '/usr/local/python/lib/python2.6/posixpath.py', line 342 in abspath
if not isabs(path):
File '/usr/local/python/lib/python2.6/posixpath.py', line 52 in isabs
return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith'
Any thoughts on how I can get rid of the partially installed freebayes tool? Or how to
troubleshoot the failing installation?
Lance
Daniel Blankenberg wrote:
>
> Hi Lance,
>
> This has to do with the way that the updating currently works. Since the migrated
version is 0.0.2, the automatic update will only update that particular Tool version
(newest version of 0.0.2). To get 0.0.3, you need to install it as a new tool. This way
you are able to have both versions installed and available e.g. for having a reproducible
rerun functionality. In the latest Galaxy-central / upcoming Galaxy-dist release, only the
newest version is shown in the lefthand tool panel.
>
> Future enhancements will include allowing the selection of different tool versions
from within the tool interface (e.g. allowing the rerun of an older version to use a newer
version) and to show and allow updating (installing) new tool versions from the same
interface (e.g. 2 to 3).
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Aug 31, 2012, at 11:47 AM, Lance Parsons wrote:
>
>> Thanks for the quick turnaround Dan. Much appreciated. When I tried to test
updating Freebayes from the toolshed, I get a message that no updates are available.
Perhaps it takes some time before they are recognized? Or am I missing something?
>>
>> Lance
>>
>> Daniel Blankenberg wrote:
>>>
>>> Hi Lance,
>>>
>>> Thank you for the pull request. I think this is an excellent way to handle
patches until the toolshed itself provides a better mechanism, particularly for the
devteam owned repositories; other repository owners may prefer different methods of
providing patches, but they can be contacted directly by using the contact form on the
toolshed. Future enhancements to the toolshed will integrate better methods of providing
this functionality, but that likely some ways off. Any suggestions and community
contributions on this would be appreciated.
>>>
>>>
>>> FreeBayes has been updated in the Toolshed to
0.9.6_9608597d12e127c847ae03aa03440ab63992fedf, with mostly minor differences from your
pull request. Please let us know if you experience any issues installing or using the
updated version (0.0.3).
>>>
>>>
>>> Thanks,
>>>
>>> Dan
>>>
>>>
>>> On Aug 30, 2012, at 11:35 AM, Lance Parsons wrote:
>>>
>>>> I have been using the FreeBayes tool in our local Galaxy instance for
some time. As FreeBayes is a rapidly evolving tool, it has been very helpful to have
Daniel Blankenberg work on keeping an updated wrapper.
>>>> Recently, I've run into a rather troublesome bug in FreeBayes
(
https://github.com/ekg/freebayes/issues/22) that is causing it to crash on nearly every
real dataset. Luckily, the bug has been fixed in the latest version of FreeBayes
(0.9.6_9608597d12e127c847ae03aa03440ab63992fedf).
>>>>
>>>> Unfortunately, the latest version has a few parameter changes that
require an update to the wrapper code. I've taken the liberty to make some changes to
the wrapper and they seem to work. However, now that I have the tool installed from the
Tool Shed, I'm not sure of the best way to 1) incorporate this update into my local
galaxy instance and 2) contribute this change back to the Tool Shed.
>>>>
>>>> The best solution is to get the Tool Shed updated and then pull that
update into my production Galaxy instance, however, I'm wondering if there is a way I
could push "hot-fixes" to my production instance without causing me headaches
down the line when the Tool Shed is inevitably updated.
>>>>
>>>> As far as coordinating updates of Tool Shed tools, I suppose the process
might be different for different tool authors. I was wondering, however, if anyone had
thoughts on how this might work best. I've created a clone of the galaxy tool shed
repository in Bitbucket (
https://bitbucket.org/lance_parsons/freebayes/) and given Daniel
and Greg access to it in hopes that would make things easier. Let me know if there is a
better way to coordinate, etc.
>>>>
>>>> Thanks again.
>>>>
>>>>
>>>> --
>>>> Lance Parsons - Scientific Programmer
>>>> 134 Carl C. Icahn Laboratory
>>>> Lewis-Sigler Institute for Integrative Genomics
>>>> Princeton University
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client. To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>
>>>>
http://lists.bx.psu.edu/
>>>
>>
>> --
>> Lance Parsons - Scientific Programmer
>> 134 Carl C. Icahn Laboratory
>> Lewis-Sigler Institute for Integrative Genomics
>> Princeton University
>>
>
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/