NGS PROJECTS

Java web server displaying SAM/BAM alignments.

Project status: beta

Author: Pierre Lindenbaum PhD. @yokofakun

Dependencies

Tested with:

• Java 1.7
• Glassfish
• JavaDB (derby)
• Picard
• apache ant
• twitter bootsrap
• vizbam library for visualizing the BAM alignments. https://github.com/lindenb/vizbam

Screenshots

Displaying a BAM like samtools tview

Displaying a SAM like samtools view

Installation

git clone "https://github.com/lindenb/ngsproject.git"
cd ngsproject.git

edit build.properties to configure the project. Something like:

asadmin=${glassfish.dir}/bin/asadmin
ivy.install.version=2.3.0
ivy.jar.dir=/commun/data/packages/ivy/jar
ivy.default.ivy.user.dir=${ivy.jar.dir}/../local
picard.version=1.87
picard.dir=/commun/data/packages/picard-tools-1.87/
vizbam=../vizbam/dist/vizbam.jar

install twitter bootsrap

ant install.bootstrap

create the database and the schema

ant start.database

create and start the server domain on glassfish

(TODO)

compile and deploy the application

ant deploy