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lines changed Original file line number Diff line number Diff line change @@ -61,6 +61,32 @@ R and Python.
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# Getting Started
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+ ## Installing ADAM via Conda
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+ ADAM is available in Conda via Bioconda, https://bioconda.github.io
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+ ``` bash
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+ $ conda install adam
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+ ```
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+ ## Installing ADAM via Homebrew
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+ ADAM is available in Homebrew via Brewsci/bio, https://github.com/brewsci/homebrew-bio
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+ ``` bash
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+ $ brew install brewsci/bio/adam
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+ ```
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+ ## Installing ADAM via Docker
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+ ADAM is available in Docker via BioContainers, https://biocontainers.pro
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+ ``` bash
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+ $ docker pull quay.io/biocontainers/adam:{tag}
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+ ```
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+ Find ` {tag} ` on the tag search page, https://quay.io/repository/biocontainers/adam?tab=tags
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## Building from Source
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You will need to have [ Apache Maven] ( http://maven.apache.org/ ) version 3.3.9 or
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You'll need to have a Spark release on your system and the ` $SPARK_HOME ` environment variable pointing at it;
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prebuilt binaries can be downloaded from the [ Spark website] ( http://spark.apache.org/downloads.html ) .
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+ As of ADAM version 0.37.0, Spark version 3.2.0 or later is required.
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# Documentation
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ADAM's documentation is available at http://adam.readthedocs.io .
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can be downloaded from the `Spark
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website <http://spark.apache.org/downloads.html> `__.
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+ As of ADAM version 0.37.0, Spark version 3.2.0 or later is required.
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Once this alias is in place, you can run ADAM by simply typing
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``adam-submit `` at the command line.
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apt-get install libgit2-dev
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The build also requires you to have the ``SparkR `` package installed,
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- where ``v2 .x.x `` should match your Spark version.
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+ where ``v3 .x.x `` should match your Spark version.
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.. code :: bash
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- R -e " devtools::install_github('apache/spark@v2 .x.x', subdir='R/pkg')"
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+ R -e " devtools::install_github('apache/spark@v3 .x.x', subdir='R/pkg')"
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The ADAM JARs can then be provided to ``SparkR `` with the following bash
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commands:
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