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 ---
#clone repository from github
#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
-
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
#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