Phylocorrelate is a phylogenetic profiling tool that detects pairs of gene/protein families with similar phylogenetic distributions. Gene co-occurrence is important to detect as it may suggest an interaction between the genes, membership in the same pathway or complex, or more general functional associations or dependencies.
This repo contains source code for building the PhyloCorrelate RShinyApp. It is currently hosted at: phylocorrelate.uwaterloo.ca
PhyloCorrelate contains pre-computed correlations for 27,372 gene families across 28,315 species, and uses the GTDB bacterial tree and gene occurrences from AnnoTree including entries from KEGG, PFAM, and TIGRFAM.
If this software proves useful in your research, please cite:
Tremblay, B.J.M., Lobb, B., and Doxey, A.C. (2021). PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling. Bioinformatics, 37(1), 17-22. DOI:10.1093/bioinformatics/btaa1105.
BLAST+Rversion 3.6.x or later
shiny, shinyWidgets, DT, shinycssloaders, igraph, plotly, visNetwork, shinythemes, ggplot2, reshape2, magrittr, promises, future, readr, gmailr, ps, fst
topGO, S4Vectors
Right now the apps send emails automatically whenever someone submits a message using the community feature. To do this, it uses local GMail keys. For obvious reasons, these are not included in the GitHub repo.
Inside the app folder is a configuration file, PhyloCorrConfig.txt. Editing this can change some of the behaviours of the app. Remember to change the file paths to match your system.
URL = "https://phylocorrelate.uwaterloo.ca/app": server app URLIndexURL = "https://phylocorrelate.uwaterloo.ca": server index URLUseBlastp = FALSE:TRUE/FALSE; enable/disable BLAST functionalityBlastpDB = "/home/$USER/phylocorrelate/blastdb/AllProteomes.faa": Location of BLAST databaseUseGmailBlastp = FALSE:TRUE/FALSE; enable/disable the server sending email for BLAST jobs via GMailServerEmail = "phylocorrelate@gmail.com": email to be used by the server to send emailsAdminEmail = "phylocorrelate@gmail.com": admin email; the server will send emails to this address in case of errors during BLAST analysesGmailCredentials = "/home/$USER/phylocorrelate/app/blastp/credentials.json": GMail credentials; look up thegmailrpackage for instructions on how to set this upGmailCache = "/home/$USER/phylocorrelate/app/blastp/.secret": GMail cache; look up thegmailrR package for instructions on how to set this upBlastpThreads = 2: number of threads to use when running BLAST
Warning: very computationally expensive.
Instructions on how to download and analyze the PFAM/TIGRFAM/KO tables go here.
shiny::runApp("app")Note: these instructions were written with Ubuntu 16.04.6 LTS in mind. They also assume you've created the log folders.
Edit your /etc/shiny-server/shiny-server.conf (replace $USER with your username):
run_as shiny;
sanitize_errors false;
preserve_logs true;
server {
listen 80;
location / {
run_as $USER;
directory_index on;
app_idle_timeout 0;
site_dir /home/$USER/phylocorrelate/index/;
log_dir /home/$USER/phylocorrelate-logs/index/;
}
location /app {
run_as $USER;
app_idle_timeout 0;
app_dir /home/$USER/phylocorrelate/app/;
log_dir /home/$USER/phylocorrelate-logs/app/;
}
}
If you ever make changes to the app, restart the server:
sudo systemctl restart shiny-server
If you've installed Shiny Server already, stop it:
sudo systemctl stop shiny-server
Install nginx and stop it:
sudo apt-get install nginx
sudo systemctl stop nginx
Now edit their configs:
# /etc/nginx/sites-available/default
server {
listen 80;
return 301 https://$host$request_uri;
}
server {
listen 443 ssl;
server_name phylocorrelate.uwaterloo.ca;
ssl_certificate /etc/letsencrypt/live/phylocorrelate.uwaterloo.ca/fullchain.pem;
ssl_certificate_key /etc/l
64A3
etsencrypt/live/phylocorrelate.uwaterloo.ca/privkey.pem;
location / {
proxy_pass http://127.0.0.1:3838;
}
}
Replace $USER with the server username:
# /etc/shiny-server/shiny-server.conf
run_as shiny;
sanitize_errors false;
preserve_logs true;
server {
listen 3838 127.0.0.1;
location / {
run_as $USER;
directory_index on;
app_idle_timeout 0;
site_dir /home/$USER/phylocorrelate/index/;
log_dir /home/$USER/phylocorrelate-logs/index/;
}
location /app-A {
run_as $USER;
app_idle_timeout 0;
app_dir /home/$USER/phylocorrelate/app/;
log_dir /home/$USER/phylocorrelate-logs/app/;
}
}
Install certbot (based on these instructions):
sudo apt-get install software-properties-common
sudo add-apt-repository ppa:certbot/certbot
sudo apt-get update
sudo apt-get install python-certbot-nginx
Run certbot:
sudo certbot --nginx
It will ask for a domain name. For example, diffbase.uwaterloo.ca. Once it's done it will tell you when the certificate will expire. When the time comes, renew it with:
sudo certbot renew
The certbot program will try and automatically modify your nginx config file. Make sure it did it correctly.
Start nginx and shiny-server:
sudo systemctl start nginx
sudo systemctl start shiny-server