SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data
All required Perl packages are installed from cpan during the install procedure, but my Stefans_Libs_Essentials which you can get from github. R packages: abind, boot, cluster, ggplot2, gplots, Hmisc, MASS, MAST, RDRToolbox, reshape, rgl, RSvgDevice, stringr, survival, vioplot Apache or any other supported web server.
The software is tested on Fedora 20 and CentOS 7.0 using apache2, and Ubuntu 16.04. It should install on any other linux distribution, too. Windows is not supported!
Obtain and install my Stefans_Lib_Essentials Perl library.
Download this source and install it using the Perl make procedure:
- cd <path to the source>
- perl Makefile.PL
- make
- make install
In addition you will need to install R and my Rscexv package as well as the python ZIFA library.
To install the server files to your web path you should use the SCexV install.pl script scripts/install.pl. This script will take care of access rights, copy all required files and changes all links inside the server files to support install into a subpath. In other words it is absolutely not recommended to copy the source files to your web path by hand. ## install.pl usagecommand line switches for install.pl
| -install_path | your server path |
| -server_user | the system user that needs to have access to all files |
| -web_root | the root of the web server - css and jscript files are installed there (default to '/var/www/html/') |
| -options | additional option for the SCexV server like randomForest 1 ncore 4 |
| -help | print this help |
| -debug | verbose output |
This script will copy the required files from <path to the source>/root into the install_path. If the web_root is not the same as the install_path all internal links are changed.
If the installed server does not work I recommend using the t/001app.t test script:
- cd <path to the source>
- perl -I lib t/001app.t
You can access our installation at stemsysbio.bmc.lu.se/SCexV/. For more help on the usage please check out our instructional videos on our YouTube channel.
sudo apt-get install libcatalyst-view-tt-perl libcatalyst-plugin-session-store-fastmmap-perl libcatalyst-plugin-session-store-cache-perl libcatalyst-plugin-redirect-perl libcatalyst-plugin-configloader-perl libcatalyst-perl libcatalyst-modules-perl libcatalyst-modules-extra-perl libcatalyst-action-rest-perl dos2unix libhtml-template-perl libnet-ssh2-perl libdatetime-format-mysql-perl libgd-svg-perl libdate-simple-perl pdl
mkdir SRC cd SRC
git clone https://github.com/stela2502/Stefans_Lib_Esentials.git cd Stefans_Lib_Esentials/Stefans_Libs_Essentials/ make sudo make install
git clone https://github.com/stela2502/SCExV.git cd SCExV/ git checkout testing cd SCExV/ make sudo make install
sudo apt-get install r-base r-base-html r-base-core libcurl4-openssl-dev libssl-dev libssh2-1-dev libx11-dev libglu1-mesa-dev libfreetype6-dev
install.packages(c('httr','git2r', 'devtools','Rcpp') )
source("http://bioconductor.org/biocLite.R") biocLite("RDRToolbox") biocLite("Biobase", 'BiocGenerics')
library(devtools) install_github('stela2502/RFclust.SGE') install_github('RGLab/MAST') install_github('stela2502/Rscexv')
sudo apt-get install python-numpy python-matplotlib python-scipy scikits.learn
cd SRC git clone https://github.com/epierson9/ZIFA cd ZIFA sudo python setup.py install
sudo apt-get install libapache2-mod-perl2 libcatalyst-engine-apache-perl apache2 libplack-perl
cpanm Plack
cd SRC/SCexV/SCexV/ sudo perl -I lib script/install.pl -install_path /var/www/html/SCexV/ -server_user www-data
This will print a sample apache2 config file that you can adjust if necessary and put into the sites_eanables directory of your apache config. ! make sure that the mod_perl2 mod is loaded !
service restart apache2
You now can access the server under http://localhost/SCexV/