[galaxy-dev] Galaxy Sample Tracking System

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[galaxy-dev] Galaxy Sample Tracking System

David Sidote
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
[hidden email]  |  732.445.4737



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Re: [galaxy-dev] Galaxy Sample Tracking System

Brad Chapman
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
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Re: [galaxy-dev] Galaxy Sample Tracking System

David Sidote
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
[hidden email]  |  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


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Re: [galaxy-dev] Galaxy Sample Tracking System

Brad Chapman
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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