Installation#

circtools is written in Python 3 (>=3.7) for most of the data processing code and R (>=4.0.0) for plotting and statistical analyses. The tool has a number of external dependencies, mostly standard bioinformatics tools and packages. The installation will, by default, try to install all required dependencies.

Installation is performed via pip install circtools or python3 setup.py install. No sudo access is required if the installation is suffixed with --user which will install the package in a user-writeable folder. In this case, the binaries should be installed to /home/$USER/.local/bin/ (for Debian-based systems).

Supported operating systems#

circtools was developed and tested on Debian Buster (10) and Ubuntu Jammy Jellyfish (22.04). macOS is supported, but still in development. However, macOS functionality cannot be fully guaranteed yet.

Installation via PyPi#

The default installation will install everything needed to run circtools except R, STAR, or Stringtie (see below). If you like you may install circtools locally (first call) or globally (second call, SU required).

python3 -m pip install circtools --user # will install only for the current user

Please note:

  • The required R libraries will be installed in the default location in your home directory - unless you set enviromnet variable $R_LIBS_USER.

  • In case want to install globally or into a dedicated ‘venv’ drop the –user option.

Installation via GitHub#

The GitHub installation will install the most recent version directly from the source repository. Use this method if you want the latest fixes and features.

git clone https://github.com/jakobilab/circtools.git
cd circtools
python3 -m pip install . --user

Installation of R dependencies#

All R packages required by circtools can be automatically installed with a single command:

circtools_install_R_dependencies

The R packages require certain development libraries installed in order to be compiled from source.

The following libraries are required (Ubuntu/Debian package names given):

  • libpng-dev

  • zlib1g-dev

  • libbz2-dev

  • libjpeg-turbo8-dev

  • libcurl4-openssl-dev

  • libxml2-dev

  • libblas-dev

  • liblzma-dev

  • libfontconfig1-dev

  • liblapack-dev

  • libssl-dev

  • libharfbuzz-dev

  • libfribidi-dev

  • libfreetype6-dev

  • libtiff5-dev

  • libjpeg-dev

A simple command to install all of these libraries on an Ubuntu/Debian system would be:

apt-get install --no-install-recommends r-base python3 python3-dev make g++ gfortran libpng-dev zlib1g-dev libbz2-dev libjpeg-turbo8-dev libcurl4-openssl-dev libxml2-dev libblas-dev liblzma-dev libfontconfig1-dev liblapack-dev libssl-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libtiff5-dev libjpeg-dev

The command above only installs the minimal required packages, no other recommend packages are installed to keep the system lean.

Installation via docker#

Docker can be used as a simple alternative to install circtools, taking care of all Python and R dependencies, thus making it well-suited for novice users. The only requirement is a working docker installation. The following command will install the latest stable version of circtools:

docker pull jakobilab/circtools

Subsequently, circtools can be run via

docker run circtools [insert arguments here]

Other than the additional command docker run circtools vs. just circtools all commands remain unchanged.

Updating circtools#

You may want to update the circtools package if new versions are published. Similar to the initial installation, there are two ways to update circtools:

pip3 install circtools --user --upgrade

cd /path/to/circtools/repo/
git pull
cd circtools/
pip3 install . install --verbose --user --upgrade

Finishing up#

In order for circtools to find all executables, the setup will add the folder /home/$USER/.local/bin/ automatically to your .bashrc file

This closes the circtools installation. To verify that circtools has been correctly installed, try to call circtools for the first time:

$> circtools --help
usage: circtools [-V] <command> [<args>]

Required dependencies#

External tools#

The primer design module as well as the exon analysis and circRNA testing module require a working installation of R with BioConductor. All R packages required are automatically installed during the setup.

Important

The setup scripts assumes that the folder for R plugins is writeable (either in the user’s home or the system folder).

Required Python packages (automatically installed)#

  • HTSeq >= 0.11.0

  • pysam >= 0.16.0.1

  • numpy >= 1.14.5

  • pybedtools >= 0.7.10

  • biopython >= 1.71

  • scipy >= 0.19.0

  • reportlab >= 3.3.0

  • pandas >= 0.25.0

  • statsmodels >= 0.9.0