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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 (>1.0) can be automatically installed if not detected.
Others have to be installed before starting the installation :
- R http://www.r-project.org/
- Python libraries :
--- bx-python (>=0.5.0) - https://pypi.python.org/pypi/bx-python
--- numpy (>=1.8.2) - http://www.scipy.org/scipylib/download.html
--- scipy (>=0.15.1) - http://www.scipy.org/scipylib/download.html
--- pysam (>=0.8.3) - https://github.com/pysam-developers/pysam
--- argparse if python <= 2.6
Note that the iced module is also required (https://github.com/hiclib/iced).
Iced is part of the HiC-Pro source code, but can also be installed independantly (>=2.2)
##
## 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 installation directory |
+---------------+------------------------------------------------------------------------+
| SAMTOOLS_PATH | Full path to the samtools installation directory (>0.1.19) |
+---------------+------------------------------------------------------------------------+
| R_PATH | Full path to the R installation directory |
+---------------+------------------------------------------------------------------------+
| PYTHON_PATH | Full path to the python installation directory (>2.7) |
+---------------+------------------------------------------------------------------------+
| CLUSTER_SYS | Scheduler to use for cluster submission. Must be TORQUE, SGE or SLURM |
+---------------+------------------------------------------------------------------------+
2 - make CONFIG_SYS=config-install.txt install