Mike;
I'm using the nglims build via "hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist" as mentioned in the wiki, Apache proxy and Postgres DB enabled.
Please correct me if any of my initial "goals" below are unattainable or if I am misinterpreting Galaxy's capabilities. I'm still attempting to learn the overall system capabilities of Galaxy and its integration between nglims samples+projects and the native Sample/Seq tracking components.
Glad to have you taking a look at the LIMS functionality. Sorry for any confusion; let me try to clear up the different options in Galaxy:
- The official functionality in Galaxy is referred to as Sample Tracking, with documentation here:
http://main.g2.bx.psu.edu/u/rkchak/p/sts
- nglims is an add-on that I'm developing; it's meant to work with the same underlying infrastructure as the sample tracking but is not an official Galaxy project. The documentation is here:
https://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims
and the fork that tracks galaxy-central, but with the nglims additions is here:
https://bitbucket.org/chapmanb/galaxy-central
Uncertainties: (1) Can samples created in the nglims section currently be tracked in the Admin tab's "Sample Tracking" area, or does the sample tracking functionality only allow tracking of the samples created with the native form definitions (within the Admin section, outside of the Lab tab "next gen sample submission")? There was a prior posting a while back that mentioning the following (verbatim)
"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."
Does this mean we're limited to creating samples outside of the nglims section if we want to track them within the native sequencing section? Secondly, will there be future support for tracking nglims-created samples with the native sample/seq tracking?
Right, so the Admin page is for dealing with Sample Tracking only, not any of the nglims. The nglims is a separate interface which has all the things you've listed built in. The 'View projects' link allows you to search samples. The 'Queues' and 'Runs' pages allow you to assign samples to flowcells and manage them through the sequencing process. So if you'd like to go the nglims route, you don't need to use the Admin page at all.
(2) How to change which sample form is used in the Lab tab's "Define samples and services". In fact, I cannot determine what form is actually used which corresponds to the form which appears when one clicks the Lab tab's "next gen sample submission".
There is a configuration file in tool-data/nglims.yaml that defines the forms. You'll also see them in the 'Manage form definitions' page since the same database tables are used, but the configuration and associated install script (scripts/nglims/add_ng_defaults.py) automate the form creation.
When creating and/or editing a form in the Admin tab's "manage form definitions", I've created a sample submission form with multiple grids, some grids which have multiple fields beneath. When editing this form and assigning fields to the respective grids, each time I save and re-edit the form, all of the fields get reset to whatever is listed as the 1st grid in the "Select the grid layout to place this field" dropdown menu, rendering all of my assigned fields to be reset to the first grid. Adding or removing a grid with the submit button also does the same thing. Any thoughts?
The nglims does not use the grid layout, but should also not reset it. If you decide to stick with sample tracking, instead of nglims, rc might be able to help you with this.
Sorry for any confusion; hope this clears things up. I'm also planning to get together a detailed overview of the nglims and automated backend processing we've put together, so hopefully more documentation will continue to make things clearer. Thanks,
Brad