"Visual and statistical analysis framework for microbial communities, and more".
This codebase contains the pre-alpha version of a statistical analysis and visualization framework that has been developed mainly for microbial community and microbial ecology studies.
Publication of this study, titled "A framework for analysis of metagenomic sequencing data", is here:
http://www.ncbi.nlm.nih.gov/pubmed/21121041
Also a static snapshot of the framework, along with some basic information about it's purpose, could be found here:
http://meren.org/framework/
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
Installation from source might be a little bit tricky for novice users.
Beta release of the Framework will provide a better installation. This part, though, is for programmers and command line enthusiasts who like to get framework running.
I tried to maintain following recipe, but this may not be the complete list of commands in order to get framework running. If you have been trying to install Viamics and if you need any help please don't hesitate to send an e-mail to:
a.murat.eren / gmail.com
Sorry for this temporary mess and inconvenience.
# APT INSTALLATION SCRIPT FOR UBUNTU/DEBIAN:
# This python script: https://raw.github.com/meren/viamics/install/install.py will
# download all dependencies and install Viamics using the apt package manager and
# other sources (cran for R packages, pip for certain python modules).
#
# After running the install script:
cd viamics/framework;python server.py # start the viamics server
cd viamics/framework/clients/ferrisweb;python manage.py runserver # start the django web interface
# go to http://localhost:8000 in your browser to try it out
--------------------------------------------------------------------------------
# The framework was developed and tested on Pardus Corporate (64 bit) version.
# It should work on any Linux distribution and even Mac, but most of the
# commands in the following section will work only on Pardus Corporate. You
# may evaluate the commands and use appropriate packages for your distro,
# but if you would like to go with Pardus Corporate, you can download it
# here:
#
# ftp://ftp.pardus.org.tr/pub/ISO/Kurulan/Corporate2/Alpha/x86_64/
#
cat /etc/pardus-release
Pardus Corporate 2 Alpha
# at this point I assume you have the codebase and you are in the root
# directory of the Framework
sudo pisi it matplotlib
sudo pisi it numeric
sudo pisi it scipy
sudo pisi it kernel-headers
sudo pisi it xorg-proto
sudo pisi it xorg-font-extra xorg-font urw-fonts
sudo pisi it make
#R
wget http://cran.opensourceresources.org/src/base/R-2/R-2.11.1.tar.gz
./configure --enable-R-shlib && make && make install
ldconfig
# run R:
sudo R
# in the R command line:
install.packages('gtools')
install.packages('gdata')
install.packages('caTools')
install.packages('bitops')
install.packages('gplots')
# quit R.
#RPy2
wget http://downloads.sourceforge.net/project/rpy/rpy2/2.1.x/rpy2-2.1.8.tar.gz
echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib64/R/bin:/usr/local/lib64/R/lib' >> ~/.bashrc
su
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib64/R/bin:/usr/local/lib64/R/lib
export PATH=$PATH:/usr/local/bin/
python setup.py install
# download RDP and put it somewhere on the disk, then edit your config file.
wget http://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.2.zip
# PyCogent
wget http://downloads.sourceforge.net/project/pycogent/PyCogent/1.4.1/PyCogent-1.4.1.tgz?use_mirror=cdnetworks-us-1
#server stuff
sudo pisi it Django
sudo pisi it apache
sudo pisi it mod_python
sudo service apache on
sudo service apache start
# configure server
# set AllowOverride All in /etc/apache2/vhosts.d/00_default_vhost.conf
# .htaccess content:
---8<---8<---8<---8<---8<---8<---8<---8<---8<-----
AddHandler mod_python .py
SetHandler python-program
Header set Pragma "no-cache"
Header set Cache-Control "no-cache"
Header set Expires "-1"
PythonPath "['/PATH/TO/FRAMEWORK/../'] + sys.path"
PythonHandler django.core.handlers.modpython
SetEnv DJANGO_SETTINGS_MODULE ferrisweb.settings
PythonDebug On
---8<---8<---8<---8<---8<---8<---8<---8<---8<-----
-
Running the server: run "python server.py" command in "framework" directory.
-
Running web client: run "python manage.py runserver" command in "framework/clients/ferrisweb/" directory, it will run a lightweighted web server you can use to connect to the framework. You will see the address in the output (or instead you can setup your Apache installation and use .htaccess file to relay web requests to the framework codebase).