Installation

Option 1: Install from source in GitHub

FitHiChIP is hosted in https://github.com/ay-lab/FitHiChIP

Open a bash terminal, go to (or create) the directory to contain the FitHiChIP source code, and then type the following command in the terminal:

git clone https://github.com/ay-lab/FitHiChIP.git

Alternatively, user can download the ZIP from GitHub, and extract.

Prerequisite softwares / packages / libraries

FitHiChIP requires the following packages / libraries to be installed first:

1. Python3 (>= version 3.4)

   • Note: Since version 9.1, FitHiChIP is upgraded to support python3 instead of the deprecated python2

   Following python libraries are to be installed:

   • OptionParser (from the library optparse; available in Python installation)

   • gzip (available in Python installation)

   • networkx (available in https://networkx.github.io/).

     Note

     Can be installed by the command pip install networkx

   • numpy (required for installing the package HiC-pro)

     Note

     Can be installed by the command pip install numpy

   • hicstraw (required for processing .hic files)

     Note

     Can be installed by the command pip install hicstraw

   • cooler (required for processing .cool or .mcool files)

     Note

     Can be installed by the command pip install cooler (or check the documentation: https://cooler.readthedocs.io/en/latest/quickstart.html#installation)

2. R (>= 3.4.3)

   Note

   User may follow https://www.datacamp.com/community/tutorials/installing-R-windows-mac-ubuntu for step by step installation of R.

   • In addition, user needs to install the following packages (needs to type the following command in an R terminal):

     install.packages(c("optparse", "ggplot2", "data.table", "splines", "fdrtool", "parallel", "tools", "plyr", "dplyr"))

   • Further, user needs to install the following Bioconductor packages:

     • GenomicRanges https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

     • EdgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html

       Note

       These two packages are required for differential analysis of FitHiChIP loops.

       User should check their R version, and Bioconductor version, to install the appropriate versions of these packages.

3. bedtools (version >= 2.26.0) http://bedtools.readthedocs.io/en/latest/

4. samtools (version >= 1.6) http://www.htslib.org/

   New in version 6.0:

   • Also install htslib (version >= 1.6) specifically for the utilities bgzip and tabix

5. Bowtie2 (available in http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

6. HiC-pro (https://github.com/nservant/HiC-Pro)

   Note

   • Required version 2.11.4 or later (we recommend using the latest version of HiCPro).

   • Upon extracting the GitHub archieve of HiC-pro, user needs to edit the file config-install.txt and specify the installed paths of mentioned packages.

   • Then, in a command line terminal, user should type the following commands:

     • make configure

     • make CONFIG_SYS=config-install.txt install

   Note

   • Installation of HiC-pro is mandatory.

7. macs2 for peak calling https://github.com/taoliu/MACS

   Note

   • To check if the above packages are installed, user can type the name of each package in the command line terminal

   • FitHiChIP is tested in linux environment, and requires bash for executing the main script.

Run FitHiChIP:

Use the following command:

bash ./FitHiChIP_HiCPro.sh -C /Your/Config/Files/Path

Option 2: Running FitHiChIP with Docker or Singularity

To not deal with any dependencies and be sure that program will execute correctly, we have prepared images for you to run your analysis in.

Choose a container system:

• Most popular option is Docker (https://www.docker.com/).

• But if you are running FitHiChIP on a cluster, you likely won't have docker installed. In that case, you can use the Singularity (https://sylabs.io/singularity/) option.

Install Docker:

If you choose to use Docker for executing FitHiChIP, you can check whether you have docker installed by typing this command in the terminal.

docker run hello-world

• If you see the hello text you are good to continue.

• If you get an error that says it couldn't connect to the Docker daemon, make sure you have the docker daemon running.

• If you get an error that says command isn't recognised, install docker by following the instructions located here: https://docs.docker.com/install/

Use Singularity

Singularity is used in environments where the users aren't trusted with the system priviliges required by Docker such as computing clusters. You can check if you have singularity installed with this command:

singularity version

If you don't have it installed in your computing environment, contact the system managers.

Get the FitHiChIP scripts from Github:

Either download the contents of FitHiChIP Github repository or clone the repository using these commands:

git clone https://github.com/ay-lab/FitHiChIP/

cd ./FitHiChIP

Run FitHiChIP:

Use one of these commands depending on your choice of using Docker or Singularity:

For Docker, use the following command:

bash ./FitHiChIP_Docker.sh -C /Your/Config/Files/Path

For Singularity, use the following command:

bash ./FitHiChIP_Singularity.sh -C /Your/Config/Files/Path

Note

Your first run will likely take longer than average as you will download the image to run FitHiChIP in.

Output:

If there are no errors, you will see a success message and FitHiChIP results will be located in the output directory you specified in the configuration file.