1. Installation

1.1. Docker image

We recommend using the latest Docker image of DROMPAplus from DockerHub as follows:

docker pull rnakato/ssp_drompa
docker run -it --rm rnakato/ssp_drompa drompa+

Note

If you are using the docker image to execute parse2wig+, it is necessary to mount the directory by -v option to access the input files as follows:

docker run -it --rm -v $(pwd):/mnt rnakato/ssp_drompa parse2wig+ \
       -i /mnt/ChIP.bam -o ChIP --odir /mnt/parse2wigdir+ --gt /mnt/genometable.txt

This command mounts the current directory to /mnt directory in the container. Please see also the document of Docker.

For Singularity:

singularity build ssp_drompa.img docker://rnakato/ssp_drompa
singularity exec ssp_drompa.img drompa+

Singularity mounts the current directory automatically. If you access the files in the other directory, please mount by --bind option, for instance:

singularity exec --bind /work ssp_drompa.img drompa+

This command mounts /work directory.

1.2. Building from source

1.2.1. Requirements

DROMPAplus requires the following programs and libraries:

  • Boost C++ library (>1.53.0)

  • Cairo libraries

  • GTK library

  • GNU Scientific Library (>1.15)

  • zlib (>1.2.7)

  • CMake (>2.8)

  • HTSlib (1.10.2) (for SAM/BAM/CRAM formatted input)

and also contains two submodules:

  • SSP

  • Coherent PDF

1.2.2. Install required libraries

On Ubuntu:

sudo apt install git build-essential libgtkmm-3.0-dev libboost-all-dev \
libgsl-dev libz-dev libbz2-dev libgsl-dev libcurl4-gnutls-dev cmake

On CentOS:

sudo yum -y install git gcc-c++ clang boost-devel zlib-devel gsl-devel gtkmm30-devel bzip2-devel cmake

On Mac:

brew install gsl gtk gtkmm cairo pkgconfig curl xz zlib boost cmake

1.2.3. Install DROMPAplus

git clone --recursive https://github.com/rnakato/DROMPAplus
cd DROMPAplus
make

1.2.4. Add the PATH

Permanently set the path to the DROMPAplus download directory by updating your ~/.bashrc file. For example, if you downloaded DROMPAplus into the $HOME directory, add the following lines to ~/.bashrc:

export PATH=$PATH:$HOME/DROMPAplus/bin:$HOME/DROMPAplus/otherbins