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| #!/bin/bash | |
| # Runs Picard tool specified on the command line, using GA4GH custom reader | |
| # for getting the data from url based INPUTs. | |
| # E.g. run_picard.sh ViewSam INPUT=<url>. | |
| # Assumes directory structure where gatk-tools-java and picard repos reside | |
| # in the same folder and client_secrets is in the same folder: | |
| # .../... | |
| # /gatk-tools-java | |
| # /picard | |
| # /client_secrets.json | |
| # If your setup is different, please modify paths below. | |
| GATK_TOOLS_JAVA_JAR=$(readlink -f `dirname $0`/../../../target/gatk-tools-java-*-SNAPSHOT-jar-with-dependencies.jar) | |
| CLIENT_SECRETS=$(readlink -f `dirname $0`/../../../../client_secrets.json) | |
| PICARD_JAR=$(readlink -f `dirname $0`/../../../../picard/build/libs/picard*all.jar) | |
| ALPN_JAR=$(readlink -f `dirname $0`/../../../lib/alpn-boot-8.1.9.v20160720.jar) | |
| echo Running Picard from $PICARD_JAR | |
| echo Using gatk-tools-java from $GATK_TOOLS_JAVA_JAR | |
| echo Using client_secrets from $CLIENT_SECRETS | |
| echo Using ALPN from $ALPN_JAR | |
| java -jar \ | |
| -Xbootclasspath/p:$ALPN_JAR:$GATK_TOOLS_JAVA_JAR \ | |
| -Dsamjdk.custom_reader=https://genomics.googleapis.com,\ | |
| com.google.cloud.genomics.gatk.htsjdk.GA4GHReaderFactory,\ | |
| $GATK_TOOLS_JAVA_JAR \ | |
| -Dga4gh.client_secrets=$CLIENT_SECRETS \ | |
| -Dga4gh.using_grpc=true \ | |
| $PICARD_JAR \ | |
| "$@" \ | |
| VERBOSITY=DEBUG QUIET=false |