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INSTALL
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INSTALL
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## 19-01-15
## Nicolas Servant
#############################
##
## HiC-Pro Installation
##
#############################
All dependencies will be checked during installation, and installed if possible.
The installation process will generate a config-system.txt file which defines all paths to HiC-Pro dependencies. Please, do not edit this file !
##
## Install Dependencies
##
Dependencies are checked during installation.
A couple of tools such as `bowtie2` and `samtools` (>=1.9) can be automatically installed if not detected.
Others have to be installed before starting the installation :
- R (http://www.r-project.org/) with the following packages
--- ggplot2 (>2.2.1)
--- RColorBrewer
--- grid
- Python (>3.7) libraries :
--- bx-python (>=0.8.8) - https://pypi.python.org/pypi/bx-python
--- numpy (>=1.18.1) - http://www.scipy.org/scipylib/download.html
--- scipy (>=1.4.1) - http://www.scipy.org/scipylib/download.html
--- pysam (>=0.15.4) - https://github.com/pysam-developers/pysam
--- argparse
Note that the iced module is also required (https://github.com/hiclib/iced).
Iced is no longer part of the HiC-Pro source code, and should be independantly installed
##
## Containers
##
If you do not want to install all dependencies manually, HiC-Pro version 3.X now provides `conda`, `Docker` and `Singularity` recipes.
### Using HiC-Pro through `conda`
In order to ease the installation of HiC-Pro dependancies, we provide a `yml` file for conda with all required tools.
In order to build your conda environment, first install [miniconda](https://docs.conda.io/en/latest/miniconda.html) and use :
```
conda env create -f MY_INSTALL_PATH/HiC-Pro/environment.yml -p WHERE_TO_INSTALL_MY_ENV
conda activate WHERE_TO_INSTALL_MY_ENV
```
### Using the HiC-Pro `Docker` image
A docker image is automatically build and available on [Docker Hub](https://hub.docker.com/repository/docker/nservant/hicpro)
To pull a Docker image, simply use :
```
docker pull nservant/hicpro:latest
```
Note that the `tag` may depend on the HiC-Pro version.
You can also build your own image from the root folder using
```
docker build -t hicpro:3.0.0 .
```
### Using HiC-Pro through `Singularity`
HiC-Pro provides a Singularity container to ease its installation process.
A ready-to-use container is available [here](https://zerkalo.curie.fr/partage/HiC-Pro/singularity_images/hicpro_latest_ubuntu.img).
In order to build you own Singularity image, use :
```
sudo singularity build hicpro_latest_ubuntu.img MY_INSTALL_PATH/HiC-Pro/envs/Singularity
```
##
## Install HiC-Pro
##
1 - Edit the config-install.txt file and set the paths. If not set, the dependencies will be sought in the $PATH and defined using the 'which' command.
+---------------+------------------------------------------------------------------------+
| SYSTEM CONFIGURATION |
+===============+========================================================================+
| PREFIX | Installation path |
+---------------+------------------------------------------------------------------------+
| BOWTIE2_PATH | Full path the bowtie2 binary |
+---------------+------------------------------------------------------------------------+
| SAMTOOLS_PATH | Full path to the samtools binary (>0.1.19) |
+---------------+------------------------------------------------------------------------+
| R_PATH | Full path to the R binary |
+---------------+------------------------------------------------------------------------+
| PYTHON_PATH | Full path to the python binary (>2.7) |
+---------------+------------------------------------------------------------------------+
| CLUSTER_SYS | Scheduler to use for cluster submission. Must be TORQUE, SGE or SLURM |
+---------------+------------------------------------------------------------------------+
2 - make CONFIG_SYS=config-install.txt install