HPRC_Assembly_Hub

Prerequisites

We are currently using an EC2 instance to serve the browser files:

• ubuntu 18.04
• t3.medium (may need to be adjusted later)
• dont assign public IP (will use elastic IP)
• storage = 800GB
• create new security group "hprc-assembly-hub"

Be sure to associate an elastic IP address to the instance as we use a DNS "A" record for hprc-browser.ucsc.edu pointing to the elastic IP.

Create The Hub

Run shell commands in:

$HUB_REPO/backbone/setup_instance.sh

(Can't be executed as a script)

These commands:

• Download this repo
• Prepares instance (minimal server setup, install Apache, redirect traffic)
• Copy Over Marina's Hub
• Install bedToBigBed

Add Tracks

bash $HUB_REPO/track_builds/dna_brnn/create_dna_brnn_track.sh
bash $HUB_REPO/track_builds/flagger/create_flagger_track.sh
bash $HUB_REPO/track_builds/sedef/create_sedef_track.sh
bash $HUB_REPO/track_builds/trf/create_trf_track.sh
bash $HUB_REPO/track_builds/repeat_masker/create_repeat_masker_track.sh
bash $HUB_REPO/track_builds/pggb_segdups/create_pggb_segdups_track.sh
bash $HUB_REPO/track_builds/alpha_sat/create_alpha_sat_track.sh
bash $HUB_REPO/track_builds/hsat2and3/create_hsat2and3_track.sh