Downloading DAWGPAWS

The current DAWGPAWS release can be downloaded from the DAWGPAWS SourceForge web site, it is also possible to check out the 'live' version of DAWGPAWS using subversion. You may either check out the entire DAWGPAWS suite via SVN, or you can browse for individual programs using the SVN browse interface. Detailed instructions for setting up the DAWGPAWS enviromnment

Download From SourceForge

The easiest way to obtain the most stable version of the DAWGPAWS programs is to download the programs from the SourceForge project downloads page.

Anonymous Checkout via SVN

An alternative way to download the DAWGPAWS program is to anonymously checkout the SVN code from the code repository on SourceForge. This will allow you to have the most recent "cutting edge" version of all of the DAWGPAWS programs and documentation. This will allow you to have the most recent bug fixes that may not have been added to the stable release and will give you access to experimental new features as they are added. These programs will be constantly changing, and using the newest versions may introduce new bugs intoyour source.

Checking out the programs via SVN will require that you have the SVN client program installed which can bedownloaded from http://subversion.tigris.org/project_packages.html. Once you have the SVN client program installed, navigate to thelocation where you want to place the DAWGPAWS program and check out thecode. This is illustrated by the following commands where the '>' symbol represents the command prompt:

  >mkdir /home/yourname/apps
  >cd /home/yourname/apps/
  >svn co https://dawgpaws.svn.sourceforge.net/svnroot/dawgpaws/trunk dawgpaws

The above command will download all the working copies of the scripts, program manuals, and emacs modes from the SourceForge repository. Thesewill be placed in the following directory structure:

dawgpaws
This base directory will be created when you check out dawgpaws for the first time

apollo
The tiers and type file for using the apollo program are installed here
docs
Additional documentation for using the DAWGPAWS program and the full text of the GNU GPL license.
emacs_modes
Major modes files for emacs, this will provide syntax highlighting to the apollo tiers file, typesfiles and configuration files.
html
This is a copy of the web pages that are hosted at http://dawgpaws.sourceforge.net

htdocs
The base directory of the html files. This includes the pages that are posted at the SourceForgeweb site.
cgi-bin
Programs run through the dawgpaws web are here.

scripts
The scripts that are the backbone of DAWGPAWS are stored in this directory
t
Test files for checking if DAWGPAWS is ready to go

data
Data files that will be used by the test scripts.

The svn 'co' command will check out the version of DAWGPAWS that is the most up to date at the time of your initial download. To update to themost recent version of DAWGPAWS at any time in the future you will need to run the svn update command from within the dawgpawsdirectory:

  >cd /home/yourname/apps/dawgpaws
  >svn update

This will update to the most current version of DAWGPAWS.

Obtaining Supported Annotation Programs

DAWGPAWS includes scripts to work with computational evidences from the following standalone programs and web services. You can get information for the following programs by clicking on the annotation program name, and you can get the documentation for the DAWGPAWS script by clicking on the script name. For full information on installing and using these programs, see the DAWGPAWS manual.

The individual annotation programs are not included in the DAWGPAWS program and must be installed separately.

GENE ANNOTATION
Program	DAWGPAWS Script
Augustus	Augustus batch_augustus.pl
BLAT	cnv_blat2gff.pl
BLAST (NCBI blastall)	batch_blast.pl batch_cnv_blast2gff.pl cnv_blast2gff.pl
EuGene	batch_eugene.pl cnv_eugene2gff.pl
EVidenceModeller (EVM)	batch_evm.pl
Fgenesh	batch_fgenesh.pl cnv_fgenesh2gff.pl
GeneMarkHMM	batch_genemark.pl cnv_genemark2gff.pl
Genscan	batch_genscan.pl
GeneID	batch_geneid.pl
PASA
SNAP	batch_snap.pl cnv_snap2gff.pl
TRANSPOSABLE ELEMENT ANNOTATION
Program	DAWGPAWS Script
LTR_STRUC	ltrstruc_prep.pl batch_ltrstruc.vbs cnv_ltrstruc2gff.pl
LTR_Finder	batch_ltrfinder.pl cnv_ltrfinder2gff.pl
find_ltr	batch_findltr.pl cnv_findltr2gff.pl
ltr_seq	batch_ltrseq.pl cnv_ltrseq2gff.pl
RepSeek	cnv_repseek2gff.pl
FINDMITE	batch_findmite.pl cnv_findmite2gff.pl
Tandem Repeats Finder	batch_trf.pl
RepeatMasker	batch_mask.pl batch_hardmask.pl cnv_repmask2gff.pl
NCBI-BLAST	batch_blast.pl batch_cnv_blast2gff.pl cnv_blast2gff.pl
TE Nest	batch_tenest.pl fetch_tenest.pl cnv_tenest2gff.pl
HMMER	batch_hmmer.pl
Mathematically Defined Repeats Requires the vmatch program	seq_oligocount.pl

Author: James Estill
Last Updated: September 28, 2011