Installation

Installing "covtobed"

Recommended way

We encourage installing covtobed via Miniconda:

conda install -c bioconda covtobed

Using Docker

To download the image:

docker pull andreatelatin/covtobed

To run the program analysing a BAM file present in the current directory:

docker run --rm -v $PWD:/data andreatelatin/covtobed covtobed /data/input.bam

Alternate methods

• Compiling from source is only recommended to experienced users at the moment. covtobed requires libbamtools-dev installed (this is the Debian package name). You should specify with -I and -l the paths to bamtools headers and library:

c++ -std=c++11 *.cpp  -I/path/to/libbamtools/  -lbamtools \
	 -o covtobed -lz

• Singularity image can be easily pulled from Docker Hub with singularity pull docker:andreatelatin/covtobed.