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how can I start a minecraft server on a server that has a web server. For example those control panels that start servers when the server is offline. I know the execute a shell script but how. If someone could provide me with some example code.

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    You said "server" 5 times in your first 2 sentences. – Batophobia Jun 25 '13 at 14:56
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So, I guess you have a Linux VPS or dedicated server, where you can install whatever you want? Good.

For this, we use the bukkit server.

Here are some instructions:

1. Download CraftBukkit's latest build: CraftBukkit - Recommended Build 
2. Put the .jar in a folder, for this example we'll use a generic one: ~/craftbukkit 
3. Move to the above directory in terminal with 'cd ~/craftbukkit' 
4. Create a new file in the minecraft folder and name it craftbukkit.sh 
5. Edit the file and paste this into it: 

#!/bin/sh BINDIR=$(dirname "$(readlink -fn "$0")") cd "$BINDIR" java -Xmx1024M -jar craftbukkit.jar -o true

6. Make the file executable, either by running "chmod +x ~/craftbukkit/craftbukkit.sh" in a terminal, or by changing the permissions in the file's properties. 
7. Then, in terminal, type '~/craftbukkit/craftbukkit.sh' to run to start the server.  
8. When you're done playing around, issue the "stop" command in console. 

You can run bukkit like described above, but there are other options - you can run the server permanently with an init script or run it with an ASCII interface

EDIT:

Reread your question, could be that I misunderstood. So here is another link to something that should be what you need - Bukkit Webby

Bukkit Webby is a lightweight web administration that is easy and fast to setup It's made of two components :

WebbyBukkitPlugin is a Bukkit Plugin that interacts with Bukkit, read your server log, find all online users, etc.

WebbyRTK is a RTK module that interacts with RemoteToolkit and run the webserver. Even if Bukkit has been shutdown, the webserver will persists and allow you to restart Bukkit.

Current Features

  • Server administration based on Bukkit Remote Toolkit (Start / Stop / Restart / Reload)
  • Online configuration files
  • Online server log
  • Backup management (manual backup, automated restore)
  • Easy installation : drop the jars and files as any bukkit plugins, setup port, login and password for webby and RTK, and you are done !
  • NO APACHE NEEDED !

There are tons of other bukkit plugins for website administration. If my suggestion is not what you want, you can check the plugins.

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