Out task is to deploy 
YouTrack on CentOS 7.X behind Nginx.
What we need to be done for that task:
- Download and install rpm with latest java from java.com
 
- Download YouTrack jar file
 
- Add new user for youtrack process and home dir for files
 
- Create youtrack.service file for systemd for youtrack service management
 
- Configure host in nginx 
 
1 and 2 need no additional comments. Only one thing, I placed youtrack jar file in /usr/local/sbin and created symlink to current version:
~ la -l /usr/local/sbin/
total 115508
-rwxr-xr-x 1 root root 118280108 Dec 9 13:42 youtrack-6.5.16953.jar
lrwxrwxrwx 1 root root 22 Dec 17 12:41 youtrack.jar -> youtrack-6.5.16953.jar
From management and security point of view it's better to create new user for new service:
useradd -m -d /opt/youtrack youtrack
Now we need .service file for youtrack in systemd:
~  cat /etc/systemd/system/youtrack.service
; /etc/systemd/system/youtrack.service
[Unit]
Description=JetBrains Youtrack
After=network.target
After=syslog.target
[Install]
WantedBy=multi-user.target
Alias=youtrack.target
[Service]
User=youtrack
Group=youtrack
PermissionsStartOnly=true
ExecStartPre=/usr/bin/mkdir -p /var/run/youtrack
ExecStartPre=/usr/bin/chown -R youtrack:youtrack /var/run/youtrack/
PIDFile=/var/run/youtrack/main.pid
ExecStart=/usr/bin/java -Xmx1g -Djava.security.egd=/dev/zrandom -Djava.awt.headless=true -Duser.home=/opt/youtrack -Djetbrains.youtrack.disableBrowser=true -jar /usr/local/sbin/youtrack.jar 127.0.0.1:4080
ExecStop=/bin/kill -HUP $MAINPID
[Install]
WantedBy=multi-user.target
Two things are important here. Since /var/run is in tempfs in CentOS 7.X you need to create pid file dir before service starting up:  
PermissionsStartOnly=true
ExecStartPre=/usr/bin/mkdir -p /var/run/youtrack
ExecStartPre=/usr/bin/chown -R youtrack:youtrack /var/run/youtrack/
And second one is youtrack's start command in:
ExecStart=/usr/bin/java -Xmx1g -Djava.security.egd=/dev/zrandom -Djava.awt.headless=true -Duser.home=/opt/youtrack -Djetbrains.youtrack.disableBrowser=true -jar /usr/local/sbin/youtrack.jar 127.0.0.1:4080
Last part is nginx config:
server {
    server_name youtrack.domain.com;
    listen 80;
    charset utf8;
    rewrite ^ https://$host$request_uri? permanent;
}
server {
    server_name youtrack.domain.com;
    listen 443 ssl;
    charset utf8;
    root /www/youtrack.domain.com/htdocs; 
    ssl on;
    ssl_certificate             /etc/nginx/ssl/youtrack.domain.com.crt;
    ssl_certificate_key         /etc/nginx/ssl/youtrack.domain.com.key;
    ssl_session_timeout         5m;
    ssl_protocols               TLSv1 TLSv1.1 TLSv1.2;
    ssl_ciphers                 ALL:!ADH:!EXPORT56:RC4+RSA:+HIGH:+MEDIUM:+LOW:+SSLv3:+EXP;
    ssl_prefer_server_ciphers   on;
    location / {
        proxy_set_header X-Forwarded-Host $host;
        proxy_set_header X-Forwarded-Server $host;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto https;
        proxy_pass http://localhost:4080/;
        client_max_body_size 64M;
    }
    access_log /var/log/nginx/youtrack.domain.comu/access.log main;
    error_log /var/log/nginx/youtrack.domain.com/error.log warn;
}