Installation

There are two alternatives for installation:

• Build a Docker image
• Installation using Python package manager

Both of them require the source code of cisCall (See Request for Download).

Build a Docker image

1. Install Docker and Docker Compose.

2. Set the environment variables for an HTTP proxy server if it exists.

   $ export http_proxy='http://example.proxy.com:8080/'
   $ export https_proxy='https://example.proxy.com:8080/'
   

3. Build an image.

   $ tar xvf /path/to/cisCall7.tar.gz --remove-files
   $ docker-compose -f cisCall7/docker-compose.yml build
   

4. Check installation.

   $ docker container run --rm ciscall --version
   

Installation using Python package manager

1. Install the following software and make their commands executable:

   • Python (>= 3.5.0) with pip
   • R (>= 4.0.0)
   • BWA (>= 0.7.15)
   • Samtools (>= 1.3.1)
   • bigWigToBedGraph

2. Install the following R packages:

   • coin
   • KernSmooth
   • RPMM
   • VGAM

   $ R -e "install.packages(c('coin', 'VGAM', 'KernSmooth', 'RPMM'), \
                            dep=T, repos='https://cloud.r-project.org/');"
   

3. Install cisCall7 using pip

   $ tar xvf /path/to/cisCall7.tar.gz --remove-files
   $ pip install -U ./cisCall7 -r ./cisCall7/requirements.txt
   

4. Check installation.

   $ ciscall --version