dzenkova/phantasus
Docker-image of phantasus web-application
Image
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dzenkova/phantasus repository overview
This project contains several tools for gene expression analysis with help of R/Bioconductor`
Installation
The package requires installing devtools package and Bioconductor library set up.
From shell do git clone with submodules:
git clone --recursive https://github.com/ctlab/phantasus
R -e 'devtools::install_github("assaron/GEOquery")' # Installing GEOquery with better caching support
R -e 'devtools::install("phantasus")'
Running
In R:
library(phantasus)
servePhantasus('0.0.0.0', 8000, cacheDir=file.path(getwd(), 'cache'))
Open http://localhost:8000 in your browser.
System dependencies
There are several system packages that have to be installed on the system. The names of these packages will be displayed during installation. On Ubuntu can install them beforehand and alltogether using command:
sudo apt-get install libapparmor-dev libprotobuf-dev protobuf-compiler libcurl4-openssl-dev
Installation example (CentOS 7)
Update packages and install R and dependencies:
yum update
yum install openssl-devel protobuf-compiler R R-Rcpp R-Rcpp-devel libcurl-devel libxml2-devel protobuf-devel git screen
Install devtools and bioclite:
R -e 'install.packages("devtools")'
R -e 'source("https://bioconductor.org/biocLite.R"); biocLite()'
R -e 'devtools::install_github("assaron/GEOquery")'
Install phantasus:
git clone --recursive https://github.com/ctlab/phantasus
R -e 'devtools::install("phantasus")'
Run phantasus at 80 port in screen:
screen -S phantasus-server
R -e 'library(phantasus); servePhantasus("0.0.0.0", 80, cacheDir="/var/phantasus/cache")'
Check http://0.0.0.0
Tag summary
Content type
Image
Digest
Size
555.9 MB
Last updated
over 5 years ago
docker pull dzenkova/phantasus