How can I serve a directory of BAM files via http most easily?

Question

[Sean Davis]

This is bordering on off-topic, but I routinely want to quickly serve up a set of BAM files to users for viewing via IGV and the like via a simple http server. Both python and node (http-server) servers do not seem to correctly support range requests. Short of configuring and running something more heavyweight (nginx, apache, etc.), are there other simple command-line http servers that can support quickly and easily serving up a directory?

[Vivek]

Any reason for not considering an FTP server? I often do range requests on 1000 genomes BAMs and it works quite well.

Answer 1

[Pierre Lindenbaum]

set-up a jetty server? see the gist below. you just have to change the path

holderPwd.setInitParameter("resourceBase", "/home/user/path/to/directory");

	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();
	}
	}
	}

view raw BamServer.java hosted with ❤ by GitHub

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

view raw example.txt hosted with ❤ by GitHub

	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 ${lib.dir}/%,%,$@)"

view raw Makefile hosted with ❤ by GitHub