Revision 6e6465755577fcc2c1124546062526d356fa9a64 authored by Vladislav Kamenev on 30 July 2018, 11:54:39 UTC, committed by Vladislav Kamenev on 30 July 2018, 11:54:39 UTC
1 parent bdd48bc
README.md
[![Travis-CI Build Status](https://travis-ci.org/ctlab/phantasus.svg?branch=master)](https://travis-ci.org/ctlab/phantasus)
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/ctlab/phantasus?branch=master&svg=true)](https://ci.appveyor.com/project/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.
```{r}
devtools::install_github("ctlab/phantasus")
```
A warning could appear that the repository contain submodules. This warning
can be safely ignored.
To install `phantasus` on R 3.4, use r-3.4 branch:
```{r}
devtools::install_github("ctlab/phantasus", ref="r-3.4")
```
## 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`:
```
R -e 'devtools::install_github("ctlab/phantasus", ref="r-3.4")'
```
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`
![swh spinner](/static/img/swh-spinner.gif)
Computing file changes ...