Species delimitation web server
Provide web interface for PTP and GMYC
Requires Django 1.11 and python 3.6
Deploy:
- Download and Install PTP
- Install X server if needed
- Clone web server into /webdata/sd_web/
- Change settings.py to the deployment enviroment: in settings.py set MEDIA_ROOT = /webdata/sd_web/sd_server/upload/ change permissions, particular for the R script copy executable (bPTP.py, summary.py and gmyc.script.R) to MEDIA_ROOT/bin
- Install R depency
- Setup Torque PBS
- python3 manage.py runserver
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
sudo apt-get install liblapack-dev liblapack3 libopenblas-base libopenblas-dev r-base-dev r-base
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.
sudo apt-get install torque-server torque-client torque-mom torque-pam torque-scheduler
/etc/init.d/torque-mom stop /etc/init.d/torque-scheduler stop /etc/init.d/torque-server stop
sudo pbs_server -t create sudo killall pbs_server
sudo echo torque.localhost > /etc/torque/server_name sudo echo torque.localhost > /var/spool/torque/server_priv/acl_svr/acl_hosts sudo echo root@torque.localhost > /var/spool/torque/server_priv/acl_svr/operators sudo echo root@torque.localhost > /var/spool/torque/server_priv/acl_svr/managers
echo "torque.localhost np=2" > /var/spool/torque/server_priv/nodes
echo torque.localhost > /var/spool/torque/mom_priv/config
sudo /etc/init.d/torque-server start sudo /etc/init.d/torque-scheduler start sudo /etc/init.d/torque-mom start
sudo qmgr -c 'set server scheduling = true' sudo qmgr -c 'set server keep_completed = 300' sudo qmgr -c 'set server mom_job_sync = true'
qmgr -c 'create queue batch' qmgr -c 'set queue batch queue_type = execution' qmgr -c 'set queue batch started = true' qmgr -c 'set queue batch enabled = true' qmgr -c 'set queue batch resources_default.walltime = 1:00:00' qmgr -c 'set queue batch resources_default.nodes = 1' qmgr -c 'set server default_queue = batch'
qmgr -c 'set server submit_hosts = torque' qmgr -c 'set server allow_node_submit = true'
sudo echo localhost > /etc/hosts.equiv
https://jabriffa.wordpress.com/2015/02/11/installing-torquepbs-job-scheduler-on-ubuntu-14-04-lts/ http://linuxtoolkit.blogspot.com/2014/06/bad-uid-for-job-execution-msgruserok.html http://docs.adaptivecomputing.com/torque/4-2-7/Content/topics/12-appendices/commandsOverview.htm