Setting up a jetty server for https://www.biostars.org/p/168197/

BamServer.java

import org.eclipse.jetty.server.*;
import org.eclipse.jetty.servlet.*;

public class BamServer {
    public static void main(String[] args) throws Exception {
        Server jettyServer = new Server(8080);
        ServletContextHandler context = new ServletContextHandler();
	context.setContextPath("/");
	DefaultServlet servlet= new DefaultServlet();

	ServletHolder holderPwd = new ServletHolder("default", servlet);
	holderPwd.setInitParameter("resourceBase", "/home/user/path/to/directory");
	context.addServlet(holderPwd, "/*");
	jettyServer.setHandler(context);

        try {
            jettyServer.start();
            jettyServer.join();
        } finally {
            jettyServer.destroy();
        }
    }
}

example.txt

$ curl -s -r 10-100 "http://localhost:8080/blastn.xml" 
ion="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nl

Makefile

lib.dir=lib

jetty.jars=$(lib.dir)/org/eclipse/jetty/jetty-servlet/9.3.6.v20151106/jetty-servlet-9.3.6.v20151106.jar:$(lib.dir)/org/eclipse/jetty/jetty-server/9.3.6.v20151106/jetty-server-9.3.6.v20151106.jar:$(lib.dir)/org/eclipse/jetty/jetty-io/9.3.6.v20151106/jetty-io-9.3.6.v20151106.jar:$(lib.dir)/org/eclipse/jetty/jetty-security/9.3.6.v20151106/jetty-security-9.3.6.v20151106.jar:$(lib.dir)/org/eclipse/jetty/jetty-util/9.3.6.v20151106/jetty-util-9.3.6.v20151106.jar:$(lib.dir)/org/eclipse/jetty/jetty-http/9.3.6.v20151106/jetty-http-9.3.6.v20151106.jar:$(lib.dir)/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar

all: $(subst :, ,${jetty.jars}) BamServer.java
	javac -cp ${jetty.jars} BamServer.java
	java -cp ${jetty.jars}:. BamServer


$(subst :, ,${jetty.jars})  : 
	mkdir -p $(dir $@) && wget -O "$@" "http://central.maven.org/maven2/$(patsubst ${lib.dir}/%,%,$@)"