This page was last updated on Sunday, 05-Nov-2017 17:18:29 CST

Installation notes for HiC-Pro version 2.9.0

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Prerequisites

• bowtie2
• Python (>2.7) with pysam (>=0.8.3), bx(>=0.5.0), numpy(>=1.8.2), and scipy(>=0.15.1) libraries
  sudo easy_install https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2
  sudo pip install --upgrade scipy
• R with the RColorBrewer and ggplot2 packages
• g++ compiler
• Samtools (>1.0)
• Unix sort (which support -V option) is required

Installation

1. $ ver=""
2. $ cd /programinstallers/
3. $ git clone https://github.com/nservant/HiC-Pro.git
4. $ cd HiC-Pro
5. Edit config-install.txt file if necessary
   $ nano config-install.txt

   #########################################################################
   ## Paths and Settings  - Start editing here !
   #########################################################################
   
   PREFIX = /usr/local/bin/hic-pro
   BOWTIE2_PATH = /usr/local/bin/bowtie2
   SAMTOOLS_PATH = /usr/local/bin/samtools1/bin
   R_PATH = /usr/bin
   PYTHON_PATH = /usr/bin
   CLUSTER_SYS =

6. $ make configure
7. $ make install
8. $ sudo make configure

   make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt
   make[1]: Entering directory `/programinstallers/HiC-Pro'
   ./scripts/install/install_dependencies.sh -c ./config-install.txt -o  /HiC-Pro_2.9.0
   Make sure internet connection works for your shell prompt under current user's privilege ...
   Starting HiC-Pro installation ...
   export /usr/local/bin/bowtie2 in PATH
   export /usr/local/bin/samtools1/bin in PATH
   export /usr/bin in PATH
   export /usr/bin in PATH
   Where should missing software prerequisites be installed ? [/usr/bin] 
   /usr/local/bin/hic-pro
   Directory /usr/local/bin/hic-pro does not exist!
   Do you want to create /usr/local/bin/hic-pro folder ? (y/n) [n] : y
   Checking dependencies ... 
   Checking Python libraries ...
   The required Python libraries appear to be already installed. 
   Checking R installation ...
   The required R packages appear to be already installed. 
   Bowtie2 Aligner appears to be already installed. 
   Samtools appears to be already installed. 
   Dependencies checked !
   Check HiC-Pro configuration ... 
   Warning : Scheduler system not defined - Default is Torque/PBS
   Configuration for TORQUE/PBS system.
   
   make[1]: Leaving directory `/programinstallers/HiC-Pro'

9. $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/hic-pro/HiC-Pro_2.9.0/bin:/usr/local/bin/hic-pro/HiC-Pro_2.9.0/bin/utils"
   …
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