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_d...
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