easy installationThe easiest and preferred way to install PyBamView is using pip:
This will install the latest stable PyBamView version listed in PyPi, and any missing libraries it depends on.
pip install pybamview
To use the "Export to PDF" feature or generate PDF snapshots using the
snapbamtool, you will also need to install rsvg-convert:
(note that the "sudo apt-get" command is assuming you're using Ubuntu/Debian. If you're using a different system you will need to use that system's package manager.)
sudo apt-get install librsvg2-bin
installing from source
requirementsFirst, make sure you have the required python packages installed:
If you want to use the "Download PDF" feature, you must have rsvg-convert installed (see above).
sudo easy_install Flask pyfasta pysam
getting the source codeObtain the source code by either:
- Downloading the tarball from github.
tar -xzvf mgymrek-pybamview-[version].tar.gz cd mgymrek-pybamview-[version]
- Cloning the git repository
git clone https://github.com/mgymrek/pybamview.git cd pybamview
building and installingAt the top of the PyBamView source directory, type:
To make sure it was installed, type:
sudo python setup.py install
and ensure that the help message comes up. Then move on to the usage page to get started!