STAR 2.5
========
Spliced Transcripts Alignment to a Reference
© Alexander Dobin, 2009-2015

AUTHOR/SUPPORT
==============
Alex Dobin, dobin@cshl.edu
https://groups.google.com/d/forum/rna-star

MANUAL
======
https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

[RELEASEnotes](RELEASEnotes) contains detailed information about the latest major release

DIRECTORY CONTENTS
==================
  * source: all source files required for compilation
  * bin: pre-compiled executables for Linux and Mac OS X
  * doc: documentation
  * extras: miscellaneous files and scripts
  * STAR-Fusion: fusion detection developed by Brian Haas, see https://github.com/STAR-Fusion/STAR-Fusion for details.
             To populate this submodule, clone STAR with `git clone --recursive https://github.com/alexdobin/STAR`
  * STAR-Fusion-x.x.x: latest release of the STAR-Fusion


COMPILING FROM SOURCE
=====================

To compile STAR from source, you must first download the latest [release](release) and uncompress it and then build it.

NOTE: The following instructions only work when obtaining the source using `git`. At least until a new
version is released which incorporates the top-level `Makefile`.

Linux
-----

```bash
# Get latest STAR source from releases
wget https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz
tar -xzf STAR_2.4.2a.tar.gz
cd STAR_2.4.2a

# Alternatively, get STAR source using git
git clone https://github.com/alexdobin/STAR.git
cd STAR

# Build STAR
make STAR

# To include STAR-Fusion
git submodule update --init --recursive

# If you have a TeX environment, you may like to build the documentation
make manual
```

Mac OS X
--------

```bash
# Get latest STAR source from releases
wget https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz
tar -xzf STAR_2.4.2a.tar.gz
cd STAR_2.4.2a

# Alternatively, get STAR source using git
git clone https://github.com/alexdobin/STAR.git
cd STAR

# To include STAR-Fusion
git submodule update --init --recursive

# Build STAR
cd source
make STARforMacStatic
```

If g++ compiler (true g++, not Clang sym-link) is not on the path, you will need to tell `make` where to find it:

```bash
# Build STAR
cd source
make STARforMacStatic CXX=/path/to/gcc
```

Developers
==========

STAR developers with write access to https://github.com/alexdobin/STAR can update the `STAR-Fusion`
submodule to a specific tag by following these steps:

```bash
git clone --recursive https://github.com/alexdobin/STAR.git
cd STAR
# or:
#
# git clone //github.com/alexdobin/STAR.git
# cd STAR
# git git submodule update --init --recursive

# checkout a specific tag for the submodule
cd STAR-Fusion
git checkout v0.3.1

# Commit the change
cd ../
git add STAR-Fusion
git commit -m "Updated STAR-Fusion to v0.3.1"

# Push the change to GitHub
git push
```


HARDWARE/SOFTWARE REQUIREMENTS
==============================
  * x86-64 compatible processors
  * 64 bit Linux or Mac OS X 
  * 30GB of RAM for human genome 


LIMITATIONS
===========
This release was tested with the default parameters for human and mouse genomes.
Please contact the author for a list of recommended parameters for much larger or much smaller genomes.

