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Add cluster command to README and reorganize sections

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mlinderm authored and fnothaft committed Sep 12, 2017
1 parent 90577e7 commit e3a0d726f67b2009f5390dbabe1c3e63c3a39840
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  1. +0 −1 README.md
@@ -111,7 +111,6 @@ We cannot package this code by default, as netlib is licensed under the LGPL and

## Running DECA in "stand-alone" mode on a workstation

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, 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.

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