Thank you for all your help that was really quick and helpful.

Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section.
Now I can create a new sequencing request and use it to add samples etc.
All this looked very good!

I was trying to follow the documentation to now to fully enable glims from here.
http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims

Now when I do this 

3. Add configured request types, forms and sample states to the database:

$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini
I get,

galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini
Traceback (most recent call last):
  File "scripts/nglims/add_ng_defaults.py", line 363, in <module>
    main(*args)
  File "scripts/nglims/add_ng_defaults.py", line 57, in main
    db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"]
KeyError: 'database_file'

 galaxy-central > python 
Python 2.5.4 (r254:67916, Oct  7 2010, 12:46:34) 
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 

also doing this I get 
galaxy-central > which python
python is /usr/local/bin/python
python is /usr/bin/python

Both are python2.5.

Almost there I think, thanks in advance.
Victor


On Oct 7, 2010, at 8:23 AM, Nate Coraor wrote:

Peter wrote:

You started Galaxy using Python 2.5, but when Galaxy
starts a child process for the python tool it would default
to the system python I think, which must still be Python 2.4.

One solution I'd try would be to hack the tool's XML file to
change <command interpreter="python"> to be explicit,
<command interpreter="python2.5">

Although I see that Brad fixed this, it's probably worth pointing out
that you wouldn't normally need to go to this much trouble.

Rather than having to edit all the tools, you can simply ensure that the
first `python` on your $PATH is the version you need.  Instructions for
this can be found as "Step 0" on http://getgalaxy.org .  You can also
use a Python virtualenv, the process for which is explained in the
production server documentation at:

 http://usegalaxy.org/production

--nate

The better fix would be in scripts/nglims/add_ng_defaults.py
to make it Python 2.4 compatible. I think this just means
replacing lines 51 and 52,

   with open(config["nglims_config_file"]) as in_handle:
       nglims_config = yaml.load(in_handle)

with:

   in_handle = open(config["nglims_config_file"])
   nglims_config = yaml.load(in_handle)
   in_handle.close()

Right Brad? ;)

Then try again, and hope that is the only thing blocking
this from working on Python 2.4. I didn't see any more
with statements so fingers crossed.

Peter

P.S. Current version is here:
http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_defaults.py

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