Hi, I have galaxy running on a local machine and I can't seem to figure out how to get the sample tracking system set up. Can anyone give me a little help to get going? Thanks, Dave ____________________________________________________ David Sidote, PhD | Director, Waksman Genomics Core Facility Waksman Institute | Rutgers University 190 Frelinghuysen Road | Piscataway, NJ 08854 dsidote@waksman.rutgers.edu | 732.445.4737
Dave;
I have galaxy running on a local machine and I can't seem to figure out how to get the sample tracking system set up. Can anyone give me a little help to get going?
Greg's presentation slides from the development conference last week are a good place to get started: http://bitbucket.org/galaxy/galaxy-central/wiki/DevConf2010 You are also very welcome to look at the sample management system I built on top of this functionality: http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims It's available as a diff against the galaxy-central head if you are tracking that. This is still a work in progress so if you are just playing and evaluating options I'd give it a try on a clean Galaxy instance. Hope this helps, Brad
Hi Brad, The sample management system you built looks great. I patched a clean instance of galaxy, install PyYAML, and then ran into this error. Do I have to create the nglims_config_file first? dsidote@ruw-172 ~/galaxy-dist > python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 336, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 51, in main with open(config["nglims_config_file"]) as in_handle: KeyError: 'nglims_config_file' Thanks so much for the help. Dave ____________________________________________________ David Sidote, PhD | Director, Waksman Genomics Core Facility Waksman Institute | Rutgers University 190 Frelinghuysen Road | Piscataway, NJ 08854 dsidote@waksman.rutgers.edu | 732.445.4737 On May 21, 2010, at 8:26 AM, Brad Chapman wrote:
Dave;
I have galaxy running on a local machine and I can't seem to figure out how to get the sample tracking system set up. Can anyone give me a little help to get going?
Greg's presentation slides from the development conference last week are a good place to get started:
http://bitbucket.org/galaxy/galaxy-central/wiki/DevConf2010
You are also very welcome to look at the sample management system I built on top of this functionality:
http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims
It's available as a diff against the galaxy-central head if you are tracking that. This is still a work in progress so if you are just playing and evaluating options I'd give it a try on a clean Galaxy instance.
Hope this helps, Brad
Dave;
The sample management system you built looks great. I patched a clean instance of galaxy, install PyYAML, and then ran into this error. Do I have to create the nglims_config_file first?
dsidote@ruw-172 ~/galaxy-dist > python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 336, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 51, in main with open(config["nglims_config_file"]) as in_handle: KeyError: 'nglims_config_file'
Thanks for giving it a try. As a first step, you might want to sanity check that the patch applied correctly: is there a tool-data/nglims.yaml file? If so, you'll want to make sure these values are in your [app:main] section of your universe_wsgi.ini file: use_nglims=True nglims_config_file=tool-data/nglims.yaml If all went well with the patch, the universe_wsgi.ini.sample should have these values. Let me know if you have any other problems, Brad
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Brad Chapman -
David Sidote