Can' Start the Galaxy instance!

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Can' Start the Galaxy instance!

xlwang
Hello,
I got an error when I installed and started a new galaxy instance just now. And I have an old version galaxy instance, it can be started and runs well, but when I updated it, the old one will get the same error like the following picture:


please help me and tell me how to fix it, thank you very much!



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Re: Can' Start the Galaxy instance!

Dannon Baker-2
I still haven't been able to reproduce this and am not sure what is wrong.  What exact version of python are you running?  Are you using a clean python environment -- virtualenv?


Can you open a python terminal and try these commands manually?

>>> import ctypes
>>> ctypes.CDLL('librt.so.1', use_errno=True)

It *should* work, yielding you something like:

<CDLL 'librt.so.1', handle 1f397b0 at 7ff73c261910>



On Wed, Jun 18, 2014 at 10:49 PM, xlwang <[hidden email]> wrote:
Hello,
I got an error when I installed and started a new galaxy instance just now. And I have an old version galaxy instance, it can be started and runs well, but when I updated it, the old one will get the same error like the following picture:


please help me and tell me how to fix it, thank you very much!



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Re: Can' Start the Galaxy instance!

Dannon Baker-2
Yeah, it definitely looks like the problem is caused by weirdness in your local Python installation.  The easiest fix is probably to set up and use a virtualenv for running Galaxy.  A compatible version of ctypes should exist as part of the python standard library for your version of python, but my guess is that your system python is using a very old pre-stdlib ctypes module.

One way to figure out which ctypes module is getting used, if you're interested, is to do the following in the python interpreter:

>>> import ctypes
>>> print ctypes.__file__



On Thu, Jun 19, 2014 at 8:28 PM, xlwang <[hidden email]> wrote:
Thank you for your reply.
my python is 2.7.3 and I didn't use virtualenv. But I used  and learned galaxy since 2012, it runs well until i installed a new instance  a few days ago.
when I run these python commands ,some errors occurred:
>>> import ctypes
>>> ctypes.CDLL('librt.so.1',use_errno=True)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: __init__() got an unexpected keyword argument 'use_errno'
>>>

Is the problem caused by python? 






At 2014-06-19 08:12:10, "Dannon Baker" <[hidden email]> wrote:
I still haven't been able to reproduce this and am not sure what is wrong.  What exact version of python are you running?  Are you using a clean python environment -- virtualenv?


Can you open a python terminal and try these commands manually?

>>> import ctypes
>>> ctypes.CDLL('librt.so.1', use_errno=True)

It *should* work, yielding you something like:

<CDLL 'librt.so.1', handle 1f397b0 at 7ff73c261910>



On Wed, Jun 18, 2014 at 10:49 PM, xlwang <[hidden email]> wrote:
Hello,
I got an error when I installed and started a new galaxy instance just now. And I have an old version galaxy instance, it can be started and runs well, but when I updated it, the old one will get the same error like the following picture:


please help me and tell me how to fix it, thank you very much!



___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/





___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/