NOTE: This instruction assumes that you already have local working biosamples service.
You can use for setting up local versions of biosamples and htsget service using build_external_libs.sh. This setting up needed only for first running. Then for deploying all required services use run_all_services.sh. You can deploy this demo manually as alternative following instructions below:
- Get from Github the EGA-dataedge project configured to run as a local servicebash
git clone -b experimental_deploy --single-branch https://github.com/Dilschat/ega-dataedge.git- Build and install ega-dataedge required tools
- Build and install picard
# Clone picard repository
git clone https://github.com/broadinstitute/picard.git
# Build and install picard locally
cd picard
gradle shadowJar
mvn install:install-file -Dfile=./build/libs/picard-2.18.11-SNAPSHOT-all.jar -DgroupId=com.github.picard -DartifactId=picard -Dversion=2.18.7-SNAPSHOT-all -Dpackaging=jar- Build and install cramtools downloading this file
# Download the cramtools file
curl -LJO -o cramtools-3.0.jar https://github.com/enasequence/cramtools/raw/master/cramtools-3.0.jar
# Build and install the cramtool files locally
mvn install:install-file -Dfile=cramtools-3.0.jar -DgroupId=com.github.cramtools -DartifactId=cramtools -Dversion=3.0 -Dpackaging=jar- Build and install ega-htsjdk
# Clone the git repository
git clone https://github.com/EGA-archive/ega-htsjdk.git
# Build and install ega-htsjdk locally
cd ega-htsjdk
mvn package -DskipTests
mvn install:install-file -Dfile=./target/ega-htsjdk-1.0-SNAPSHOT.jar -DgroupId=eu.elixir.ega.ebi -DartifactId=ega-htsjdk -Dversion=1.0-SNAPSHOT -Dpackaging=jar
- Run htsget service using an IDE or in docker container:
#run htsget
docker-compose up -d htsgetNote that the HTSGET service will run on port 8086
- Run biosamples
#run biosamples
cd biosamples-v4-demo
sudo ./docker-integration.sh
# run example
curl localhost:8081/biosamples/samples/ga4gh?disease=lukemia&page=0