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Add tutorial command listing to the README
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mlinderm committed Jun 9, 2019
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Expand Up @@ -113,7 +113,7 @@ We cannot package this code by default, as netlib is licensed under the LGPL and

A small dataset (30 samples by 300 targets) is distributed as part of the [XHMM tutorial](http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml).
An example DECA command to call CNVs from the [pre-computed read-depth matrix and related files](http://atgu.mgh.harvard.edu/xhmm/RUN.zip)
on a 16-core workstation with 128 GB RAM is below. Note that you will need to set the `DECA_JAR` environment variable to point to the jar file created by `mvn package`, set `spark.local.dir` to a suitable temporary directory for your system and likely need to change the executor and driver memory to suitable values for your system. The `exclude_targets.txt` and `DATA.RD.txt` files from the XHMM tutorial data are also distributed as part of the DECA test resources in the `deca-core/src/test/resources/` directory.
on a 16-core workstation with 128 GB RAM is shown below; a step-by-step listing of the commands to call CNVs in the tutorial data is available [here](TUTORIAL.md). Note that you will need to set the `DECA_JAR` environment variable to point to the jar file created by `mvn package`, set `spark.local.dir` to a suitable temporary directory for your system and likely need to change the executor and driver memory to suitable values for your system. The `exclude_targets.txt` and `DATA.RD.txt` files from the XHMM tutorial data are also distributed as part of the DECA test resources in the `deca-core/src/test/resources/` directory.

From within the unzip'd RUN directory, prepare `exclude_targets.txt`:

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