Victor; Thanks much for playing with nglims. Glad things are working well for you with the interface and you are on to results processing.
Nice work on the new updates of nglims. We like that we can now build a flowcell. We know see a results form. How do we configure this form to show the results as well as the default plots we know see in the default layout?
The results are uploaded by the automated processing pipeline, which is available from:
https://github.com/chapmanb/bcbb/tree/master/nextgen
This generates fastq files as runs come off the sequencer, transfers them to the Galaxy machine, does alignments and other analysis steps like SNP calling, and then uploads the results to Galaxy.
As part of that process, statistics on clusters and passing clusters are uploaded for display in the results and plots. This helps us monitor how things are going with the machine and diagnose issues.
Happy to help with setting this up if you have any issues. The GitHub page has some basic documentation to get started.
And also is it possible to add a data library to a project without using the native tracking request from the admin tab? We typically use one file per lane say the s_1_sequence.txt.
What we do is have users report a lab group or affiliation when they create a Galaxy account, and then assign them permissions to a Data Library folder associated with that lab. When uploading, the fastq and other files go within a sub-folder of that library named by the date of the run. We get a lot of new users trying to submit requests who don't yet understand Data Libraries, so this workflow eases the learning curve for them.
I'm finishing up a new entry page that supports assigning barcodes to samples which should be ready next week, and then hope to write up documentation so knowing the areas where you are running into issue is really helpful.
Thanks much, Brad