Installation

Use CLIPipe Docker

Prepare reference demo and docker

Download the reference, demo data, and CLIPipe docker to your own directory, and unzip:

 mkdir clipipe_test;
 cd clipipe_test;
 wget http://clipipe.ncrnalab.org/clipipe_ref.tar.gz;
 wget http://clipipe.ncrnalab.org/clipipe_demo.tar.gz;
 wget http://clipipe.ncrnalab.org/CLIPipe_v1.0.3_.tar.gz;
 tar -xvzf clipipe_ref.tar.gz;
 tar -xvzf clipipe_demo.tar.gz;

Run CLIPipe Docker

Docker provides an easy way to run CLIPipe in a working environment that is completely separated from your host machine. All required software and packages are already installed in a ready-to-use image of CLIPipe docker, so there are no more requirements. You can use the docker image we provide: CLIPipe Docker Image. And you may execute these commands to get the docker CLIPipe_1.0.X container:
```
 cd clipipe_test;
 docker import CLIPipe_v1.0.3_.tar.gz zs/clipipe:1.0.3_test     ##import the docker

 docker run --name=CLIPipe_1.0.3_test -t -d -h CLIPipe_docker --restart unless-stopped -v <the-absolute-path-of-current-directory>:/home/CLIPipe_user/clipipe zs/clipipe:1.0.3_test /bin/bash
```
- Using -v <the-absolute-path-of-current-directory>:/home/CLIPipe_user/clipipe, we map the directory the-absolute-path-of-current-directory in host machine, where the data used the analysis resides (make sure to use absolute path), to directory /home/CLIPipe_user/clipipe inside docker container. Both, path to the folder on the host machine and path within the container (/home/CLIPipe_user/clipipe) must be absolute.
To show the docker container CLIPipe_1.0.3_test, you can execute:
```
 docker container ls
```

To execute the container CLIPipe_1.0.3_test, you can execute:

 docker exec -it CLIPipe_1.0.3_test bash

 cd /home/CLIPipe_user/clipipe;
 find clipipe_demo  -type d  -exec chmod 777 {} \;
 find clipipe_demo  -type f -exec chmod 666 {} \;

After entering the container, please change the user to CLIPipe_user
```
 su CLIPipe_user;
 cd ~
```

To test the installation and get information about the command-line interface of CLIPipe, you can execute:

 clipipe --help

A helper message is shown like this:

 usage: clipipe [-h] --user_config_file USER_CONFIG_FILE
                {pre_process,mapping,peak_calling}

 CLIPipe: A comprehensive quality control and analysis pipeline for CLIP highthroughput sequencing data
 =======================================================================================================
 CLIPipe is a Python module and associated command-line interface (CLI), which provides all the
 commands needed to process protein-RNA CLIP interaction data and to identify and quantify
 sites of protein-RNA interactions on RNA.

 CLIPipe's main input are FASTQ files with iCLIP sequencing data, its main output are BED files
 with identified cross-linked sites.

 A number of analyses are included in CLIPipe that provide insights into the properties of
 protein-RNA interaction.

 optional arguments:
    -h, --help                show this help message and exit
    -u, --user_config_file    the user config file

 positional arguments:
    {pre_process,mapping,peak_calling}

 =======================================================================================================
 For additional help or support, please visit https://github.com/ShangZhang/clipipe

Use from source

We have hide the details of each step using Snakemake and you only need to run one single command. However, you can use some of the codes if you are familiar with snakemake. The source code is here.