circtools is written in Python2 (>= 2.7,
reconstruct module) and Python3 (>=3.4, all other modules). 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 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 Jessie 8 64 Bit and Debian Stretch 9 64 bit. macOS support is currently (09/2018) being tested and is already available in the
mac-dev branch of the github repository (however, the macOS functionality cannot be fully guaranteed yet).
Installation from PyPi (preferred)¶
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).
pip3 install circtools --user
- The required R libraries will be installed in the default location in your home directory - unless you set enviromnet variable $R_LIBS_USER.
- In case want to install globally or into a dedicated ‘venv’ drop the –user option.
Installation from GitHub¶
The GitHub installation will install the most recent version directly from the source repository. Use this method if you want the latest fixes and features.
git clone https://github.com/dieterich-lab/circtools.git cd circtools pip3 install . --verbose --user
You may want to update the circtools package if new versions are published. Like for the initial installation there are two ways to update circtools:
pip3 install circtools --user --upgrade
cd /path/to/circtools/repo/ git pull pip3 install . install --verbose --user --upgrade
- bedtools [>= 2.27.1] required by the enrichment module
- R [>= 3.3] required by visualisation scripts and the primer design module
- STAR [>= 2.6.0] required by the
reconstructmodule to map RNA-seq reads against a reference genome and detect back splice junctions
- Stringtie [>= 1.3.3b, optional] required by the
exonmodule to carry out exon level analyses.
The installation procedure will automatically install two additional Python-based dependencies: DCC and FUCHS by temporarily cloning the repositories and installing both tools via setuptools to
/home/$USER/.local/bin/. Both tools require Python 2 in order to run.
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.
The setup scripts assumes that the folder for R plugins is writeable (either in the user’s home or the system folder).
- For circRNA detection
- For circRNA reconstruction
- For circRNA enrichment
- For circRNA primer design
Getting the source code¶
Step 1: Clone source code from GitHub:
git clone https://github.com/dieterich-lab/circtools.git
Step 2: Install circtools using the provided installation script. The
--user flag installs circtools in your home folder, thus making sure you do not require any administrative rights during the installation:
cd circtools pip3 install . install --verbose --user
Step 3: Setting up R environment. In order for the automatic installation of R packages to work we need to set the package directory to a user-writeable path. The setup automatically sets that path to
Step 5: Adding installation folder to
$PATH. In order for circtools to find all executables, the setup will add the folder
/home/$USER/.local/bin/ automatically to your
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>]