Obtaining and installing StringTie
----------------------------------

The current version of StringTie can be downloaded from
  http://ccb.jhu.edu/software/stringtie
  
In order to build StringTie from the source package,
the following steps should be taken:

* Unpack the downloaded StringTie source archive in a directory of your choice, e.g.:

cd ~/src/
tar xvfz ~/Downloads/stringtie-V.V.V.tar.gz

A directory called stringtie-V.V.V (where V.V.V is the current
numeric version of the program) will be created in the current directory.

* Change to that directory and build the stringtie executable:

cd stringtie-V.V.V
make release

Note that simply running `make` will produce an executable which is more
suitable for debugging and runtime checking but which can be significantly
slower than the optimized version which is obtained by using the 
`make release` command.

Running StringTie
-----------------

Run stringtie from the command line like this:

stringtie [options] <aligned_reads.bam>

The main input of the program is a SAMtools BAM file with RNA-Seq alignments
sorted by genomic location (for example the `accepted_hits.bam` file produced
by TopHat).

A list of parameters and options for the program can be obtained by running
the program with only the -h or --help option.

More detailed usage instructions can be found on the StringTie website: 
http://ccb.jhu.edu/software/stringtie

