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.
Goals I'm trying to accomplish: (1) Create a fresh custom sample form in the Admin tab's "Manage Form Definitions" to use in the Lab tab's (nglims section) "next gen sample submission" process, and assign this custom sample form to be used as the "default" form when creating a new sample in nglim section's "next gen sample submission", (2) Allow multiple/various defined samples created with this custom sample submission form to be submitted in the Lab tab's "Submit samples as a project" as a project for tracking in the Admin tab section, (3) Allow "Find Samples" in the Admin tab to potentially query for nglims samples created with this sample form.
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?
(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".
Additional concern: 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?
Galaxy appears to be a very promising product and we're looking forward to having the researchers and sequence team use this environment, once we finalize the configuration and push into production. I'm sure I'll have additional questions once I work through some of these current issues. My apologies for the extended length of this post and if I've somehow misinterpreted some of the functionalities and compatibilities.
Thanks in advance for your feedback.
Best Regards, Mike