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Add conda, homebrew, biocontainers installation docs.
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heuermh committed Jan 24, 2022
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29 changes: 29 additions & 0 deletions README.md
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Expand Up @@ -61,6 +61,32 @@ R and Python.

# Getting Started

## Installing ADAM via Conda

ADAM is available in Conda via Bioconda, https://bioconda.github.io

```bash
$ conda install adam
```

## Installing ADAM via Homebrew

ADAM is available in Homebrew via Brewsci/bio, https://github.com/brewsci/homebrew-bio

```bash
$ brew install brewsci/bio/adam
```

## Installing ADAM via Docker

ADAM is available in Docker via BioContainers, https://biocontainers.pro

```bash
$ docker pull quay.io/biocontainers/adam:{tag}
```

Find `{tag}` on the tag search page, https://quay.io/repository/biocontainers/adam?tab=tags

## Building from Source

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;
prebuilt binaries can be downloaded from the [Spark website](http://spark.apache.org/downloads.html).

As of ADAM version 0.37.0, Spark version 3.2.0 or later is required.


# Documentation

ADAM's documentation is available at http://adam.readthedocs.io.
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6 changes: 4 additions & 2 deletions docs/installation/source.rst
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Expand Up @@ -35,6 +35,8 @@ will need to have the Spark binaries on your system; prebuilt binaries
can be downloaded from the `Spark
website <http://spark.apache.org/downloads.html>`__.

As of ADAM version 0.37.0, Spark version 3.2.0 or later is required.

Once this alias is in place, you can run ADAM by simply typing
``adam-submit`` at the command line.

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apt-get install libgit2-dev
The build also requires you to have the ``SparkR`` package installed,
where ``v2.x.x`` should match your Spark version.
where ``v3.x.x`` should match your Spark version.

.. code:: bash
R -e "devtools::install_github('apache/spark@v2.x.x', subdir='R/pkg')"
R -e "devtools::install_github('apache/spark@v3.x.x', subdir='R/pkg')"
The ADAM JARs can then be provided to ``SparkR`` with the following bash
commands:
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