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STAR

Spliced Transcripts Alignment to a Reference.

Interactive Usage

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrsh command.

The latest version of STAR (currently 2.5.0c) is made available with the command

module load apps/gcc/5.2/STAR

Alternatively, you can load a specific version with

module load apps/gcc/5.2/STAR/2.5.0c

This command makes the STAR binary available to your session and also loads the gcc 5.2 compiler environment which was used to build STAR. Check that STAR is working correctly by displaying the version

STAR --version

This should give the output

STAR_2.5.0c

Documentation

The STAR manual is available online: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

Installation notes

STAR was installed using gcc 5.2

module load compilers/gcc/5.2

mkdir STAR
mv ./STAR-2.5.0c.zip ./STAR
cd ./STAR/
unzip STAR-2.5.0c.zip
cd STAR-2.5.0c
make
cd source
mkdir -p /usr/local/packages6/apps/gcc/5.2/STAR/2.5.0c
mv ./STAR /usr/local/packages6/apps/gcc/5.2/STAR/2.5.0c/

Testing

No test suite was found.

Modulefile

  • The module file is on the system at /usr/local/modulefiles/apps/gcc/5.2/STAR/2.5.0c

It’s contents

#%Module1.0#####################################################################
##
## STAR 2.5.0c module file
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

module load compilers/gcc/5.2

module-whatis   "Makes version 2.5.0c of STAR available"

set STAR_DIR /usr/local/packages6/apps/gcc/5.2/STAR/2.5.0c/

prepend-path PATH $STAR_DIR