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Preparing Hadoop

OpenCGA uses dependencies from Hortonworks HDP-2.5.0 internally. It has not been tested with other flavours of Hadoop.

You can use one of the many available hadoop sandboxes provided by Hortonworks or Cloudera or downloading and installing manually the required Hadoop components: Hadoop, Spark, HBase, Phoenix

Preparing OpenCGA

Download or pull the version you want to try.

git clone https://github.com/opencb/opencga.git
cd opencga

You can build the application from sources executing:

mvn clean install -DskipTests -Dstorage-hadoop -Popencga-storage-hadoop-deps

You can customize some configuration parameters adding them to the compilation with -D<param>=<value>. Some interesting params are:

  • OPENCGA.INSTALLATION.DIR  for changing the installation directory.
  • OPENCGA.CLIENT.REST.HOST  This parameter indicates the address of the REST server. For this tutorial we are going to use a embedded REST server.
  • OPENCGA.CELLBASE.REST.HOST to specify the cellbase installation.
  • OPENCGA.CELLBASE.VERSION to specify the cellbase version.
  • OPENCGA.STORAGE.DEFAULT_ENGINE to specify the default storage engine. By default is "mongodb", so we will need to add --storage-engine hadoop to each command. Compile with -DOPENCGA.STORAGE.DEFAULT_ENGINE=hadoop to avoid that.

To see the rest of the configurable parameters, check the default-config profile at the main pom.xml.

For example, to change the default engine and the rest host, execute:

mvn clean install -DskipTests -Dstorage-hadoop -Popencga-storage-hadoop-deps -DOPENCGA.STORAGE.DEFAULT_ENGINE=hadoop  -DOPENCGA.CLIENT.REST.HOST=http://localhost:9090/opencga

Then copy the application (the content of build folder) into the installation directory, by default and in this tutorial this is /opt/opencga.

mkdir /opt/opencga
cp ./build/* /opt/opencga

Needless to say, the computer where opencga is installed must have access to the Hadoop cluster.

In order to interact with Hadoop, we need to provide the configuration files. In OpenCGA There are two ways for doing that, depending on the way of accessing to Hadoop.

a) Hadoop node. Full access.

This configuration is for hadoop client nodes (or local installations, or hadoop nodes) where the commands 'hadoop', 'yarn' and 'hbase' are installed, and the client configuration updated. The script bin/opencga-env.sh will add the configuration files to the java classpath. Nothing else is needed.

In this scenario, you will be able to execute this commands:

hadoop classpath
hbase classpath

b) External server. Read only.

In other case, we need to obtain the configuration files from the cluster hadoop. In this scenario, just copy the configuration files in a folder called etc in the installation directory. This folder is automatically added to the classpath. With this configuration, you will only be able to execute queries.

Start OpenCGA

To simplify the installation, we are going to use the embedded server for the REST API.

# Set up opencga
## Install OpenCGA
./opencga-admin.sh catalog install --secret-key not_so_secret_key  --algorithm HS256 <<< admin_P@ssword

## Start servers
mkdir p ../logs/
./opencga-admin.sh server rest --start -p <<< $CATALOG_ADMIN_PASSWORD \
                 2>> ../logs/daemon.err \
                 >> ../logs/daemon.out &
./opencga-admin.sh catalog daemon --start -p <<< $CATALOG_ADMIN_PASSWORD \
                 2>> ../logs/server.err \
                 >> ../logs/server.out &

## Create our first user
./opencga-admin.sh users create -u platinum --user-email platinum@illumina.com \
                 --user-name Platinum \
                 --user-organization Illumina \
                 --user-password $USER_PASSWORD \
                 --password <<< $CATALOG_ADMIN_PASSWORD

Indexing a VCF file

For this testing area, we are going to use a sample VCF data from the Platinum genomes. You can use any other file, but all the examples below use the VCF file platinum-genomes-vcf-NA12877_S1.genome.vcf.gz

You can find other files to load in this link: http://swdev.bioinfo.hpc.cam.ac.uk/downloads/datasets/vcf/platinum_genomes/gz/

Once OpenCGA is installed and running, we need to create a new project and study in catalog, and register our VCF file. You can also download all the files from that link

# Create study and folder structure
./opencga.sh users login -u platinum -p <<< $USER_PASSWORD
./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
wget 'http://swdev.bioinfo.hpc.cam.ac.uk/downloads/datasets/vcf/platinum_genomes/gz/platinum-genomes-vcf-NA12877_S1.genome.vcf.gz'
./opencga.sh files link -s platinum -i /path/to/platinum/vcf/* --path 10_input


Once everything is set up, just need to load the files. This command line will create an internal job that will be executed by the catalog daemon.

# Index asynchronously via Daemon all the files in the folder 10_input
./opencga.sh files index --file 10_input --outdir 20_transformed --load

Optionally, we can use the opencga-analysis.sh command line for a synchronous execution:

# Index synchronously all the files in the folder 10_input
mkdir /tmp/opencga_job
./opencga-analysis.sh variants index --file 10_input --outdir /tmp/opencga_job --path 20_transformed

Without Catalog

For testing porpouses, it may be interesting to have an standalone installation of OpenCGA-Storage.You can find another build folder at opencga/opencga-storage/build/ that contains only the binaries for storage

A simple indexation can be done executing the next command:

./opencga-storage.sh variant index --storage-engine hadoop --study-id 1 --study-name platinum --gvcf --database opencga_platinum -i /path/to/platinum/vcf/*

Annotate the variants database.

At this point, the last but not least, is annotate the variants. Despite this can be done at the same time than indexing variant files, it may be more clear in separated executions:

./opencga-analysis.sh variant annotate -o . --study platinum 


This will annotate all the variants without annotation at the database, skipping the already annotated variants.

Querying variants

And we are done! At this point we will be ready to query variants. Here are some examples commands:

  • Count number of variants
./opencga.sh variant query --study platinum --count
  • Get the first 10 variants from the Chromosome 8
./opencga.sh variant query --study platinum --region 8 --limit 10 --sort
  • Count variants in gene BRCA2
./opencga.sh variant query --study platinum --gene BRCA2 --count

You can find the full list of options at the help:

./opencga.sh variant query --help


You can find other query examples at this other tutorial: Querying Variants with the Command Line

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