Revision e13e02cb8e6c65da545fb67c41b9eb3e5f9bdcd0 authored by Vladislav Kamenev on 19 February 2019, 20:27:22 UTC, committed by Vladislav Kamenev on 19 February 2019, 20:27:22 UTC
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README.md
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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.
## 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 all together using command:
```{bash}
sudo apt-get install libapparmor-dev libprotobuf-dev protobuf-compiler libcurl4-openssl-dev libssl-dev libxml2-dev
```
## Docker
To simplify deployment phantasus Docker image can be used. It is build regularly and is available at https://hub.docker.com/r/dzenkova/phantasus
You can run with the following commands:
```{bash}
docker pull dzenkova/phantasus
docker run -t -d -p 80:80 dzenkova/phantasus
```
Phantasus will be available at http://localhost
## Docker compose
Docker compose is available [here](docker-compose.yml)
You can run with the following command:
```{bash}
docker-compose up -d
```
Phantasus will be available at http://localhost
## ARCHS4
Phantasus tries to find ARCHS4 .h5 files at cacheDir/archs4
There are three different ways to obtain ARCHS4 files depending on how you are running Phantasus:
### Bare install
You can download ARCHS4 (~10GB) with the following command:
```{bash}
R -e 'library(phantasus); updateARCHS4("path/to/cacheDir/archs4")'
```
Don't forget to specify the path to cacheDir/arcsh4.
### Docker-compose (preferred way)
If you are running phantasus using our docker-compose then you can easily download ARCHS4 (~10GB) with the following command:
```{bash}
docker-compose run phantasus R -e 'library(phantasus); updateARCHS4();'
```
If you happen to have ARCHS4 already downloaded on your PC then you can just sepcify path to folder in archs4 volume at docker-compose.yml
### Docker
If you are running phantasus in docker then you can download ARCHS4 (~10GB) with the following command:
```{bash}
docker exec -it phantasus_container R -e 'library(phantasus); updateARCHS4();'
```
Where "phantasus_container" is the name or hash of running container with phantasus.
Beware that downloading ARCHS4 without volumes makes no sense (see docker-compose.yml).
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