Awesome
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