mpnst_surveyor

The MPNST Surveyor is a database for displaying genomic analysis from the sequencing of MPNST tumors. Please visit the NF Research Initiative website to learn more.

The website can currently be reached at http://18.206.76.181:8000/

Details:

Made using R Shiny, styled with HTML and CSS.

Deployed on AWS r4 EC2 instance, instructions below ---

Prerequisites:

• docker

Set Up:

#clone repository from github

• git clone https://github.com/parklab/mpnst_surveyor.git

#enter working directory of the repo

• cd mpnst_surveyor

#create docker image from within mpnst_surveyor directory

• docker build -t mpnst_app .

#after container 'mpnst_app' is built, add in the necessary data files as volumes. Because of the size of these directo

Data volumes to have on instance (available on EBI Cluster)

• bamsnap_INDEL.tar.gz
• bamsnap_SNV.tar.gz
• consensus_SNV_all_samples.rds

Unpack tar files

• tar -xvf bamsnap_INDEL.tar.gz

• tar -xvf bamsnap_SNV.tar.gz

leave all these files/directories in the home directory /home/ubuntu or adjust next statement for dir location

---

Run with Docker

#docker command to add volumes and run on port 8000: (may have to copy each line individually)

sudo docker run -it –rm -p 8000:8000 \
-v /home/ubuntu/bamsnap_SNV:/srv/shinyapps/mpnst_app/www/SNV_reads/bamsnap_SNV \
-v /home/ubuntu/bamsnap_INDEL:/srv/shinyapps/mpnst_app/www/INDEL_reads/bamsnap_INDEL \
mpnst_app

#(OR) docker command to deploy to port 80

sudo docker run -it –rm -p 80:8000 \
-v /home/ubuntu/bamsnap_SNV:/srv/shinyapps/mpnst_app/www/SNV_reads/bamsnap_SNV \
-v /home/ubuntu/bamsnap_INDEL:/srv/shinyapps/mpnst_app/www/INDEL_reads/bamsnap_INDEL \
mpnst_app