semi-automatic classification and postprocessing of LTR retrotransposons
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README

Prerequisites
-------------

LTRsift needs the GTK+ version 2 library to work. If you are on a Linux desktop
system (e.g. Ubuntu Linux, Red Hat, SuSE, ...), it is very likely that this
library is already installed.
On Mac OS X, however, it is not and needs to be installed. This can, for
instance, be done using a package manager like Fink (http://www.finkproject.org).
First install the Fink environment according to the instructions at
http://www.finkproject.org/download/srcdist.php.  After the self-update, the
command

$ fink install cairo gtk+2-dev

should suffice to build and install the required libraries. This will take
some time!

Quick Start
-----------

In this directory, run the following in a terminal:

$ ./run_ltrsift

This will run LTRsift with default settings, requiring LAST (and/or BLAST)
to be installed in the system search path.

To try out LTRsift with the supplied sample data in the
sample_data/ directory, please consult the README file in that
directory for necessary preparation steps.

Running LTRsift (binary distribution)
-------------------------------------

To use LTRsift, run the ``ltrsift'' executable in the bin/
subdirectory of the binary distribution. This requires that a
current version of the GenomeTools library (http://genometools.org)
is installed and can be found (e.g. by installing it in a system-wide
location).

If no GenomeTools library is present, or if you do not want to install it,
run the ``ltrsift_static'' executable instead. This version does not require
any installed version.

The LAST binaries (lastal and lastdb) should be located in the system
search path. If they are not, is it possible to specify their location
using the ``GT_LAST_PATH" environment variable prior to running LTRsift.
The same applies for the BLAST location. Use ``GT_BLAST_PATH'' to specify
the full path to the ``blastall'' executable.

Style files (describing how the linear diagram of the candidate features
look like) can be set via the LTRSIFT_STYLE_FILE environment variable.
A sensible default style is built into LTRsift.

Example filtering rules
-----------------------

Some sample filtering rules (as described in the LTRsift paper)
can be found in the filters/ subdirectory.

Building LTRsift from source
----------------------------

This section is only relevant if you want to compile a version of
LTRsift by yourself. To run the binary executable version, this step is
not required.

You need to have the GenomeTools shared library installed in a location
accessible by the dynamic linker. Installing GenomeTools system-wide as
described in the GenomeTools INSTALL file should suffice.
If a system-wide install is not possible, you can specify your
GenomeTools installation directory by setting the environment variable
``gt_prefix'' to the appropriate directory prior to building LTRsift.

Invoke GNU make, e.g.:

$ make [argument ...]

to build LTRsift. You need at least version 3.80 of GNU make, you can check
which version you have by invoking

$ make --version

On *BSD GNU make is often called ``gmake''.

Possible arguments:

- 64bit=yes to compile a 64-bit version (not available on all platforms)
- opt=no to disable optimization
- static=yes to build a static version as well (called ``ltrsift_static'')

Example call to build LTRsift without assertions on a system where GNU make
is called ``gmake'':

$ gmake assert=no


Enjoy!