https://github.com/berquist/star

RNA-seq aligner

https://github.com/berquist/star

Repository

RNA-seq aligner

https://github.com/berquist/star/blob/master/

STAR 2.7.11b
==========
Spliced Transcripts Alignment to a Reference
 Alexander Dobin, 2009-2024
https://www.ncbi.nlm.nih.gov/pubmed/23104886

AUTHOR/SUPPORT
==============
Alex Dobin, dobin@cshl.edu 

https://github.com/alexdobin/STAR/issues 

https://groups.google.com/d/forum/rna-star

HARDWARE/SOFTWARE REQUIREMENTS
==============================
  * x86-64 compatible processors
  * 64 bit Linux or Mac OS X

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

[RELEASEnotes](https://github.com/alexdobin/STAR/blob/master/RELEASEnotes.md) contains detailed information about the latest major release
[CHANGES](https://github.com/alexdobin/STAR/blob/master/CHANGES.md) contains detailed information about all the changes in all releases

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

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

Download the latest [release from](https://github.com/alexdobin/STAR/releases) and uncompress it
--------------------------------------------------------

```bash
# Get latest STAR source from releases
wget https://github.com/alexdobin/STAR/archive/2.7.11b.tar.gz
tar -xzf 2.7.11b.tar.gz
cd STAR-2.7.11b

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

Compile under Linux
-------------------

```bash
# Compile
cd STAR/source
make STAR
```
For processors that do not support AVX extensions, specify the target SIMD architecture, e.g.
```
make STAR CXXFLAGS_SIMD=sse
```


Compile under Mac OS X
----------------------

```bash
# 1. Install brew (http://brew.sh/)
# 2. Install gcc with brew:
$ brew install gcc
# 3. Build STAR:
# run 'make' in the source directory
# note that the path to c++ executable has to be adjusted to its current version
$cd source
$make STARforMacStatic CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
# 4. Make it availible through the terminal
$cp STAR /usr/local/bin
```

All platforms - non-standard gcc
--------------------------------

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
cd source
make STARforMacStatic CXX=/path/to/gcc
```

If employing STAR only on a single machine or a homogeneously setup cluster, you may aim at helping the compiler to optimize in way that is tailored to your platform. The flags LDFLAGSextra and CXXFLAGSextra are appended to the default optimizations specified in source/Makefile.
```
# platform-specific optimization for gcc/g++
make CXXFLAGSextra=-march=native
# together with link-time optimization
make LDFLAGSextra=-flto CXXFLAGSextra="-flto -march=native"
```

FreeBSD ports
=============

STAR can be installed on FreeBSD via the FreeBSD ports system.
To install via the binary package, simply run:
```
pkg install star
```

LIMITATIONS
===========
This release was tested with the default parameters for human and mouse genomes.
Mammal genomes require at least 16GB of RAM, ideally 32GB.
Please contact the author for a list of recommended parameters for much larger or much smaller genomes.


FUNDING
=======
The development of STAR is supported by the National Human Genome Research Institute of
the National Institutes of Health under Award Number R01HG009318.
The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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