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semi-automatic classification and postprocessing of LTR retrotransposons
License: GNU General Public License v2.0
This project forked from satta/ltrsift
semi-automatic classification and postprocessing of LTR retrotransposons
License: GNU General Public License v2.0
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!
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