deploy_opencga_local.sh

#!/bin/bash

name=${1:opencga}

if [ "$name" != "opencga" ]; then 
        name=opencga_$name 
fi 
echo "Installation name :" $name

echo "Clean installation dir"
mkdir -p ~/opt/${name}/libs
rm -rf ~/opt/${name}/libs

echo "Copy libs and conf"
cp -r build/* ~/opt/${name}

echo "Copy war"
cp build/*.war ~/opt/tomcat/webapps/

install_demo_opencga.sh

#!/bin/bash

# Compile and deploy opencga rc3
cd ~/appl/opencga
mvn clean install -DskipTests -Dopencga.name=$OPENCGA_NAME ; ./deploy_opencga_local.sh $OPENCGA_NAME

cd ~/opt/opencga_$OPENCGA_NAME/bin
mkdir -p ../logs

# Set up opencga
./opencga-admin.sh catalog install -p --algorithm HS256 --secret-key aaaa <<< admin
./opencga-admin.sh users create -u platinum --email platinum@illumina.com --name Platinum --organization Illumina --user-password PlatinumP@ss --password <<< admin
./opencga-admin.sh catalog daemon --start -p <<< admin 2>> ../logs/daemon.err >> ../logs/daemon.out &

# Create study and folder structure
./opencga.sh users login -u platinum -p <<< PlatinumP@ss
./opencga.sh projects create --alias platinum --name Platinum --organism-scientific-name "homo sapiens" --organism-assembly GRCh37
./opencga.sh studies create --project platinum --alias platinum --name Platinum
./opencga.sh files create-folder -s platinum --path 10_input
./opencga.sh files create-folder -s platinum --path 20_transformed
./opencga.sh files create-folder -s platinum --path 30_load
./opencga.sh files create-folder -s platinum --path 40_annotation
./opencga.sh files tree -s platinum --folder .

# Link files
./opencga.sh files link -s platinum -i ../examples/variant-test-file.vcf.gz --path 10_input 
./opencga.sh files link -s platinum -i ../examples/1k.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz --path 10_input

# Index via Daemon
./opencga.sh variant index --file 10_input --outdir 20_transformed --transform
./opencga.sh variant index --file 10_input --outdir 30_load --load -Dmerge.ignore-overlapping-variants=true -Dmerge.batch.size=1

./opencga-admin.sh catalog daemon --stop

settings.xml

<settings>
    <profiles>

         <profile>
            <id>catalog_prefix</id>
            <activation>
                <property>
                    <name>opencga.name</name>
                </property>
            </activation>
            <properties>
                <opencga.war.name>opencga_${opencga.name}</opencga.war.name>

                <OPENCGA.DB.PREFIX>opencga_${opencga.name}</OPENCGA.DB.PREFIX>
                <OPENCGA.INSTALLATION.DIR>${user.home}/opt/opencga_${opencga.name}</OPENCGA.INSTALLATION.DIR>
                <OPENCGA.USER.WORKSPACE>${OPENCGA.INSTALLATION.DIR}/sessions/</OPENCGA.USER.WORKSPACE>
                <OPENCGA.JOBS.ROOTDIR>${OPENCGA.CATALOG.ROOTDIR}/jobs/</OPENCGA.JOBS.ROOTDIR>

                <OPENCGA.CATALOG.DB.HOSTS>localhost:27017</OPENCGA.CATALOG.DB.HOSTS>
                <OPENCGA.CATALOG.DB.DATABASE>opencga_catalog_${opencga.name}</OPENCGA.CATALOG.DB.DATABASE>

                <OPENCGA.STORAGE.VARIANT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.VARIANT.DB.HOSTS>
                <OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>

                <OPENCGA.CLIENT.HOST>http://localhost:8080/${opencga.war.name}</OPENCGA.CLIENT.HOST>

                <OPENCGA.SERVER.REST.PORT>9090</OPENCGA.SERVER.REST.PORT>
                <OPENCGA.SERVER.GRPC.PORT>9091</OPENCGA.SERVER.GRPC.PORT>
              
            </properties>
        </profile>
    </profiles>
</settings>