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I am switching my server's hosting provider from Windows Server to Linux Debian and I need help to convert my Run.bat to an executable shell script.

The Windows batch file:

java -cp bin; deps/mail.jar; deps/xstream.jar; deps/xpp3-1.1.4c.jar;
deps/scheduling.jar -server server.Server

When I save this as a shell script it does not properly run when I "Run in terminal", the shell just opens and closes immediately.

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In linux, the separator is : instead of ;, so try this instead:

$ java -cp bin:deps/mail.jar:deps/xstream.jar:deps/xpp3-1.1.4c.jar:deps/scheduling.jar -server server.Server

Copy the command without the $. The $ is used to indicate the command belongs in a linux shell.

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