Merge pull request #21 from paulmenzel/improve-readme

Juicer is currently in its beta release, Juicer version 1.5.

For general questions, please use

[the Google Group](https://groups.google.com/forum/#!forum/3d-genomics).

If you have further difficulties using Juicer, please do not

hesitate to contact us (theaidenlab@gmail.com)

and >= 64 GB RAM (min 16 GB RAM)

Juicer currently works with the following resource management software:

- OpenLava (http://www.openlava.org/)

- LSF (http://www-03.ibm.com/systems/services/platformcomputing/lsf.html)

- SLURM (http://slurm.schedmd.com/download.html)

- [OpenLava](http://www.openlava.org/)

- [LSF](https://www.ibm.com/systems/spectrum-computing/products/lsf)

- [SLURM](https://slurm.schedmd.com/download.html)

- GridEngine (Univa, etc. any flavor)

### Juicer tools requirements

(version >= 1.7) on Windows, Linux, and Mac OSX.  We recommend using the

latest Java version available, but please do not use the Java Beta Version.

Minimum system requirements for running Java can be found at

http://java.com/en/download/help/sysreq.xml

https://java.com/en/download/help/sysreq.xml

To download and install the latest Java Runtime Environment (JRE), please go

to http://www.java.com/download

to https://www.java.com/download

### GNU CoreUtils

### CUDA (for HiCCUPS peak calling)

You must have an NVIDIA GPU to install CUDA

Instructions for installing the latest version of CUDA can be found

on the NVIDIA Developer site:

   https://developer.nvidia.com/cuda-downloads

You must have an NVIDIA GPU to install CUDA.

Instructions for installing the latest version of CUDA can be found on the

[NVIDIA Developer site](https://developer.nvidia.com/cuda-downloads).

The native libraries included with Juicer are compiled for CUDA 7 or CUDA 7.5.

See the [download page for Juicer Tools](https://github.com/theaidenlab/juicer/wiki/Download)

See the [download page for Juicer

Tools](https://github.com/theaidenlab/juicer/wiki/Download).

Other versions of CUDA can be used, but you will need to download the

respective native libraries from

   http://www.jcuda.org/downloads/downloads.html

[JCuda](http://www.jcuda.org/downloads/downloads.html).

For best performance, use a dedicated GPU. You may also be able to obtain

access to GPU clusters through Amazon Web Services or a local research

### Building new jars

See the Juicebox documentation at <https://github.com/theaidenlab/Juicebox> for details on building new jars of the juicer_tools.

See the Juicebox documentation at <https://github.com/theaidenlab/Juicebox> for

details on building new jars of the juicer_tools.

------------

Quick Start

```

java -jar juicer_tools.jar (command...) [flags...] <parameters...>`

```

There are different flavors of juicer_tools that depend on the CUDA version.  If you do not use GPUs, these versions are equivalent. Otherwise, juicer_tools.X.X.jar uses CUDA version X.X 

There are different flavors of juicer_tools that depend on the CUDA version.

If you do not use GPUs, these versions are equivalent. Otherwise,

juicer_tools.X.X.jar uses CUDA version X.X

For HiCCUPS loop calling without the shell or bat script, you will need to

call:

   By default, these are located in the lib/jcuda folder.

In the command line tools, there are several analysis functions:

		`apa` for conducting aggregate peak analysis  

		`hiccups` for annotating loops  

		`motifs` for finding CTCF motifs  

		`arrowhead` for annotating contact domains  

		`eigenvector` for calculating the eigenvector (first PC) of the Pearson's

		`pearsons` for calculating the Pearson's

1.  `apa` for conducting aggregate peak analysis

1.  `hiccups` for annotating loops

1.  `motifs` for finding CTCF motifs

1.  `arrowhead` for annotating contact domains

1.  `eigenvector` for calculating the eigenvector (first PC) of the Pearson's

1.  `pearsons` for calculating the Pearson's

The `juicer_tools` (Unix/MacOS) script can be used in place of the unwieldy

		`java -Djava.library.path=path/to/natives/ -jar juicer_tools.jar`