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# Dockerfile for sideRETRO
A pipeline for detecting Somatic Insertion of DE novo RETROcopies
## Getting Started
These instructions will cover installation and usage information for the docker container.
### Prerequisities
In order to run this container you'll need docker installed.
* [Windows](https://docs.docker.com/windows/started)
* [OS X](https://docs.docker.com/mac/started/)
* [Linux](https://docs.docker.com/linux/started/)
### Acquiring sideRETRO Image
#### Manual Installation
Clone **sideRETRO** repository:
`$ git clone https://github.com/galantelab/sideRETRO.git`
Inside `sideRETRO/` folder:
`$ docker build -t sider -f docker/Dockerfile .`
#### Pulling Image
Pull **sideRETRO** image from [dockerhub](https://hub.docker.com) registry:
`$ docker pull galantelab/sider`
It's possible to pull a specific image version by appending a colon with the required tag.
For example:
`$ docker pull galantelab/sider:dev`
For a complete list of **sideRETRO** versions, please access the dockerhub tag page: <https://hub.docker.com/r/galantelab/sider/tags/>
### Setting
Mac users may need to change the default settings in order to make use
of all CPUs and memory. For a complete tutorial, see: [Get started with Docker Desktop for Mac](https://docs.docker.com/docker-for-mac/#preferences-menu)
### Usage
#### Container Examples
`$ docker run galantelab/sider`
By default **sideRETRO** runs in a container-private folder. You can change this using flags, like user (-u),
current directory, and volumes (-w and -v). E.g. this behaves like an executable standalone and gives you
the power to process files outside the container:
```
$ docker run \
--rm \
-u $(id -u):$(id -g) \
-v $(pwd):$(pwd) \
-w $(pwd) \
galantelab/sider ps -a exon.gff in.bam
```
How to get a shell started in your container:
`$ docker run -ti --entrypoint bash galantelab/sider`
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