Thank you RC. I now have a data library and a folder within the data library associated to a sample which was submitted by using the Lab tab (part of nglims). Attached is a snapshot of a sample that I created via the lab tab. Say as an admin I now create a sequencing request. How do I choose the samples submitted by the Lab tab? I see I can specify a sample name. But, I think we want/need to add the samples that were already set by the Lab tab. Sorry if I'm not understanding the workflow. I think it would be great if Researchers can submit samples as listed in the Lab tab section. Then the sequencing team can create a run with those samples that . In our case 7 or 8 samples per flowcell (illumina GAII). That way al the meta data from those samples that were entered via the Lab tab can be tracked by the researchers and the sequencing team. Does that make sense? Thank you. Victor On Nov 24, 2010, at 3:02 PM, Ramkrishna Chakrabarty wrote:
Victor,
The data library select field lists all publicly available data libraries and the one's the sequencing request owner can access. So, if you create a data library which is public to all Galaxy users or is accessible to the user who owns the sequencing request, then that data library should show up in the select field against the sample.
We are working on adding a 'create new data library' feature on the edit samples page, which would be available in the near future.
rc
On Nov 24, 2010, at 3:49 PM, Victor Ruotti wrote:
Thank you Brad for your response. We now have a the nglims system in place. We can allow the submission of samples via the Lab tab. Also, the project shows up in the tracking request form via the admin tab.
I do have a question that is the only thing stopping us from fully implementing nglims. How do we associate a data library to samples. We tried creating a data library for storing all of our runs and having a hard time associating a data library with a sample. Attached is a snapshot of the page. We tried setting the permissions and still cant see the data libraries under the sample. Any ideas?
Thanks again for all you help. Very impressed with all as always. Victor
On Nov 22, 2010, at 3:11 PM, Brad Chapman wrote:
Victor and rc; Victor, the nglims extension on top of rc's work compartmentalizes the form generation into the YAML configuration in tool-data/nglims.yaml. The setup script (scripts/nglims/add_ng_defaults.py) uses this to fill in the form information programatically, and then the controller uses this to sort out naming in managing the samples.
This all uses rc's form infrastructure, so the editing with Manage Forms will work fine.
This is probably not as generalized as it could be so there will be some hidden naming dependencies depending on what you're planning to do. Let me know if you run into issues with that aspect,
Brad
Victor,
The form definitions can be modified by an admin in Manage Forms in the admin view. Click on 'Edit' popup menu next to any form name to modify form name, description or its fields.
Thanks rc
On Nov 22, 2010, at 1:59 PM, Victor Ruotti wrote:
Hi, We have a question about NGLIMS. How do we go and where do we go to change things. For example the default sample submission forms etc. Thanks in advance. Victor
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