Here is a JSch example to SSH login (password) a remote server and runs a shell script.

package com.mkyong.io.howto;

import com.jcraft.jsch.*;

import java.io.IOException;
import java.io.InputStream;

public class RunRemoteScript {

    private static final String REMOTE_HOST = "1.1.1.1";
    private static final String USERNAME = "";
    private static final String PASSWORD = "";
    private static final int REMOTE_PORT = 22;
    private static final int SESSION_TIMEOUT = 10000;
    private static final int CHANNEL_TIMEOUT = 5000;

    public static void main(String[] args) {

        String remoteShellScript = "/root/hello.sh";

        Session jschSession = null;

        try {

            JSch jsch = new JSch();
            jsch.setKnownHosts("/home/mkyong/.ssh/known_hosts");
            jschSession = jsch.getSession(USERNAME, REMOTE_HOST, REMOTE_PORT);

            // not recommend, uses jsch.setKnownHosts
            //jschSession.setConfig("StrictHostKeyChecking", "no");

            // authenticate using password
            jschSession.setPassword(PASSWORD);

            // 10 seconds timeout session
            jschSession.connect(SESSION_TIMEOUT);

            ChannelExec channelExec = (ChannelExec) jschSession.openChannel("exec");

            // run a shell script
            channelExec.setCommand("sh " + remoteShellScript + " mkyong");

            // display errors to System.err
            channelExec.setErrStream(System.err);

            InputStream in = channelExec.getInputStream();

            // 5 seconds timeout channel
            channelExec.connect(CHANNEL_TIMEOUT);

            // read the result from remote server
            byte[] tmp = new byte[1024];
            while (true) {
                while (in.available() > 0) {
                    int i = in.read(tmp, 0, 1024);
                    if (i < 0) break;
                    System.out.print(new String(tmp, 0, i));
                }
                if (channelExec.isClosed()) {
                    if (in.available() > 0) continue;
                    System.out.println("exit-status: "
                         + channelExec.getExitStatus());
                    break;
                }
                try {
                    Thread.sleep(1000);
                } catch (Exception ee) {
                }
            }

            channelExec.disconnect();

        } catch (JSchException | IOException e) {

            e.printStackTrace();

        } finally {
            if (jschSession != null) {
                jschSession.disconnect();
            }
        }

    }
}

Refer to this example How to run a remote shell script in Java

Yes, but probably not in the way you are thinking.

You need to copy the script over to the remote system.

Check out http://seancode.blogspot.com.au/2008/02/jsch-scp-file-in-java.html who's written a FileSender wrapper that might help

You could also check out Copying a file in sftp with jsch library just out of interest

You could also check out the included examples http://www.jcraft.com/jsch/examples/ (knew they were there somewhere)

The problem is that the shell redirection (<) sends the file over the ssh tunnel. And the Java class is expecting not the file, but a string with the "filename" of a local file that will be read with a FileReader.

Instead of passing the filename to the FileReader, read from the standard input.

InputStreamReader isReader = new InputStreamReader(System.in);
BufferedReader iR  = new BufferedReader (isReader);

Used this as a reference: https://stackoverflow.com/questions/5724646/how-to-pipe-input-to-java-program-with-bash

Now your class will be:

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileReader;
import java.io.OutputStreamWriter;
import java.io.InputStreamReader;

public class ReadFirstLine 
{
    public static void main(String[] args) throws Exception 
    {
       String filename = args[0];
       System.out.println(filename);

       //BufferedReader iR  = new BufferedReader (new FileReader(filename));
       InputStreamReader isReader = new InputStreamReader(System.in);
       BufferedReader iR  = new BufferedReader (isReader);

       BufferedWriter oW = new BufferedWriter(new OutputStreamWriter(System.out));

       //outputWriter.write(iR.readLine());
       System.out.println(iR.readLine());

       iR.close();
       oW.close();
    }
}

But for this task I would definitely use instead:

head -1 filename.txt

:)

Check out Jsch or Ganymed SSH. I have used the latter to perform ssh/scp tasks programmatically.