ngsCAT can be downloaded from the following link:
See detailed instructions about manual installation of ngsCAT and its dependencies in section 3.3.1 of the online documentation. For an automatic installation, see “Installation scripts” below.
UPDATE!: visit the new docker section to run ngscat in a few seconds!
With the aim of making the installation of ngsCAT and its dependencies easier, installation scripts for different Unix-based distributions are provided. These scripts automatically download and install ngsCAT source code and its dependencies (see section 3.3.2 in the online documentation). Choose proper script according to your distribution:
The following sinthetic examples have been run with ngsCAT (see section 7 of the online documentation).
Three whole-exome experiments taken from the 1000 genomes project are run through ngsCAT (see section 8 in the online documentation):
We have developed a docker image to run ngscat without any manual installation. Please visit our repository in dockerhub: https://hub.docker.com/r/clinbioinfosspa/ngscat
If you are interested in build your own docker image, have a look to the dockerfile:
FROM debian:wheezy RUN apt-get update && apt-get -y install python zlibc zlib1g zlib1g-dev samtools python-numpy python-scipy python-xlwt python-matplotlib wget curl RUN wget -O - https://bootstrap.pypa.io/get-pip.py -o get-pip.py|python RUN pip install 'requests[security]' pysam==0.7.6 pybedtools==0.8.0 progressbar==2.5 WORKDIR / RUN wget -O - http://ngscat.clinbioinfosspa.es/_media/ngscat/download/ngscat.v0.1.tar.gz | tar xzf - RUN ln -s /ngscat.v0.1 ngscat && chmod +x /ngscat/ngscat.py RUN echo "backend: agg" > /etc/matplotlibrc ENTRYPOINT ["/ngscat/ngscat.py"]