Beginner's Guide to the GMS Web Viewer
- Introduction
- Models
- Searching and Filtering
- Model Details
- Processing Profiles
- Processing Profile Details
- Instrument Data
- Instrument Data Details
- Subjects
- Subject Details
- Builds
- Build Details
- Workflow Stderr
- Workflow Stdout
- Build Data Directory
- Apache Configuration and Security
The GMS comes pre-installed with a fully functional web viewer. The web viewer is configured as a ruby on rails app with apache server. It is accessible by default at http://localhost.
The app allows rapid searching and filtering of models, builds, processing profiles, instrument data and subjects. It also allows convenient browsing of data directories for all builds at http://localhost/data/. This tutorial will walk through screenshot examples of many of the views available.
The main page (Models) of the GMS webviewer (shown below) defaults to the list of current models in the GMS database. It shows the model names and their corresponding processing profile. Clicking on the Model Name takes a user to the Model Details Page for that model. Similarly, clicking on a Processing Profile Name takes a user to the corresponding Processing Profile Details Page. Additional tabs show similar views for Processing Profiles, Instrument Data, Subjects, Builds.
Each of the main tabs in the GMS web viewer has a live filtering/searching box in the upper right corner. In the example shown below models are being filtered to show only those with the phrase 'Somatic' in their name. This filtering works on any text or sub-text in any displayed column.
Clicking on a Model Name or Model ID from any page in the web viewer will take a user to the corresponding Model Details page (shown below). The Model Details page is broken into several sections. (1) The Model Attributes section lists the Model ID, User, Creation Date, and links to the corresponding Subject Details page and Last Completed [Build Details] (#build-details) page and Data Directory. (2) The Processing Profile section lists the corresponding Processing Profile for this Model with a link to the Processing Profile Details page. (3) The Inputs sections list the inputs for the model. In this case we are looking at a Somatic Variation Exome model. Its inputs include an annotation build, normal and tumor reference alignment builds, and a previously discovered variations build. (4) The builds section lists all the builds attempted for this model with their Build IDs, run status, dates scheduled and completed along with links to the corresponding Build Details page and Data Directory.
The second tab of the web viewer displays a simple list of the Processing Profiles available in the GMS database (shown below). Each Processing Profile Name is linked to its corresponding Processing Profile Details page.
Clicking on a Processing Profile Name or ID from any page in the web viewer will take a user to the corresponding Processing Profile Details page (shown below). As described this details the specific parameters that define a processing profile. In this example we are looking at the Processing Profile for Somatic Variation Exome.
The third tab of the web viewer displays the list of the Instrument Data currently imported in the GMS database (shown below). Each piece of Instrument Data is associated with a library and has an ID that is linked to its corresponding Instrument Data Details page.
Clicking on an Instrument Data Name or ID from any page in the web viewer will take a user to the corresponding Instrument Data Details page (shown below). In this case, the instrument data corresponds to a single lane (lane 8) of Illumina data with flowcell D1VCPACXX, ~171 million clusters, consisting of 100bp reads and imported as a bam file.
The default apache configuration hosts the gms web viewer app at http://localhost and serves all data in /opt/gms/ at http://localhost/data/
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