https://github.com/ctlab/phantasus
Revision 39967c9a88f4c169b766cdbbf52b0342bed595f2 authored by Alexey Sergushichev on 27 February 2018, 08:17:25 UTC, committed by Alexey Sergushichev on 27 February 2018, 08:17:25 UTC
1 parent a3aadad
Tip revision: 39967c9a88f4c169b766cdbbf52b0342bed595f2 authored by Alexey Sergushichev on 27 February 2018, 08:17:25 UTC
trying to fix os-x build
trying to fix os-x build
Tip revision: 39967c9
README.md
[![Travis-CI Build Status](https://travis-ci.org/ctlab/phantasus.svg?branch=master)](https://travis-ci.org/ctlab/phantasus)
[![codecov](https://codecov.io/gh/ctlab/phantasus/branch/master/graph/badge.svg)](https://codecov.io/gh/ctlab/phantasus)
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:
```{shell}
git clone --recursive https://github.com/ctlab/phantasus
R -e 'devtools::install("phantasus")'
````
## Running
In R:
```{r}
library(phantasus)
servePhantasus('0.0.0.0', 8000, cacheDir='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:
```{bash}
sudo apt-get install libapparmor-dev libprotobuf-dev protobuf-compiler libcurl4-openssl-dev libssl-dev libxml2-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", repos="https://cloud.r-project.org")'
R -e 'source("https://bioconductor.org/biocLite.R"); biocLite()'
```
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`
Computing file changes ...