Victor;
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?
You probably don't want to mix the "nglims" approach with Galaxy's native sample tracking functionality. While I've build the nglims part to use the same database tables and be fairly interoperable, it does take some different data representation choices, especially with regards to the sample/request relationship. Apologies if this is confusing; I can answer below from the nglims approach here, and rc can hopefully provide more background from the native Galaxy sample tracking approach.
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?
In nglims, you want to associate a user in the sequencing team with the"sequencing" role using the standard Admin tools to manage roles. This user will then have additional menu options in the left panel when you go to Lab->Next gen sample submission. Specifically, the Queues link allows these users to manage samples as they come in. They move the samples through various steps in tandem with things happening in the lab: Awaiting Sample -> Pre-sequencing quantitation -> Sequencing Once they are in the sequencing step, you can prepare a flowcell and associate samples with lanes using a drag and drop interface. So in this view, the queues manage various samples as they come in and then the 'Prepare flow cell' step associates them with a sequencing run. Hope this helps, Brad