Species delimitation web server

Provide web interface for PTP, GMYC, CROP and UCLUST

Deploy: Change settings.py to the deployment enviroment

See this page how to install and configure X server: http://pythonhosted.org/ete2/tutorial/tutorial_webplugin.html#servers https://groups.google.com/forum/#!searchin/etetoolkit/x$20server$20/etetoolkit/XSIeQyX9W64/0mPc4n1SrDMJ

Add this to /etc/apache2/httpd.conf: FastCGIExternalServer /webdata/sd_web/sd_server/sd_server.fcgi -host 193.197.73.70:2222

Add this to /etc/apache2/sites-enabled/000-default: <VirtualHost :80> ServerName species.h-its.org DocumentRoot /webdata/sd_web/sd_server #alias /static /webdata/sd_web/sd_server/static #alias /download /webdata/sd_web/sd_server/download RewriteEngine On RewriteRule ^/(static.)$ /$1 [QSA,L,PT] #RewriteRule ^/(download.)$ /$1 [QSA,L,PT] RewriteCond %{REQUEST_FILENAME} !-f RewriteRule ^/(.)$ /sd_server.fcgi/$1 [QSA,L]

export DISPLAY=localhost:0.0 python manage.py runfcgi method=threaded host=193.197.73.70 port=2222

sudo service apache2 restart

INSTALL R GMYC: install.packages("ape",repos="http://cran.r-project.org/") install.packages("paran",repos="http://cran.r-project.org/") install.packages("splits",repos="http://R-Forge.R-project.org")

$Rscript gmyc.script.R tree method

input: an input tree in newick or nexus format (its name should end with ".tre" or ".nex". method: type of method, s for single and m for multiple threshold.

(you can make it executable if Rscript is installed as /usr/bin/Rscript, like other linux scripts)

It outputs following files.

xxxx_list: a tab-delimited text file of delimitation. it is an output of the spec.list function. xxxx_summary: a text file of summary of analysis from summary.gmyc. xxxx_plot.pdf: plots in pdf format. xxxx_plot.png: plots in png format.

I think you should install r-base-dev as well as r-base to use Rscript command.