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