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:
Build and install phenopackets
- Build phenopacket-schema from the github repository and following
the building instructions. NOTE that you should get the specific commit with hash
c67527e48f94fa71e8763c3a2a3234917b5c5bcb.
# Building and installing phenopackets
git clone https://github.com/phenopackets/phenopacket-schema.git
cd phenopacket-schema
# Get specific commit fot avoiding errors before release
git reset --hard c67527e48f94fa71e8763c3a2a3234917b5c5bcb
mvn clean install- Install built jar as local lib from the phenopacket-shchema:
# Install the package on your local machine
mvn install:install-file -Dfile=./target/phenopacket-schema-0.0.7-SNAPSHOT.jar -DgroupId=org.phenopackets.schema.v1 -DartifactId=phenopacket-schema -Dversion=0.0.7-SNAPSHOT -Dpackaging=jar- 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 your terminal for using that in biosamples. Note that the HTSGET service will run on port 8080
-
Run biosamples
#run biosamples
cd biosamples-v4-demo
sudo ./docker-integration.sh
# run example
curl localhost:8081/biosamples/samples/ga4gh?disease=lukemia&page=0