Installation

circtools is written in Python3 (>=3.4). 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).

circtools was developed and tested on Debian Jessie 8 64 Bit. macOS support is currently (08/2018) being tested and is already available in the mac-dev branch of the github repository (however, the macOS functionality cannot be fully guaranteed yet).

Quick 3-line installation

The default installation requires running python on the command line and will install everything needed to run circtools except bedtools and R (see below):

git clone [email protected]:dieterich-lab/circtools.git
cd circtools
python3 setup.py install --verbose --user

Required dependencies

External tools

Important

Currently at least bedtools v2.26.0-125-g52db654-dirty is required to run the enrichment module. Earlier versions have issues with the shuffle command.

  • R [>= 3.3] required by visualisation scripts and the primer design module

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/

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).

Python packages

  • For circRNA detection
    • HTSeq>=0.6.1
    • pysam>=0.9.0
    • numpy>=1.8.2
    • pandas>=0.18.1
  • For circRNA reconstruction
    • HTSeq>=0.6.1
    • pysam>=0.9.0
    • numpy>=1.8.2
    • pathos>=0.2.1
  • For circRNA enrichment
    • pybedtools>=0.7.10
    • statsmodels>=0.8.0
  • For circRNA primer design
    • BioPython>=1.71

Detailed installation

Getting the source code

Step 1: Clone source code from GitHub:

git clone [email protected]:dieterich-lab/circtools.git

Installation

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
python3 setup.py install --verbose --user

R environment

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 can automatically set that path to /home/$USER/.R/:

Should we update the R package location in order to install package as user?
Update R_LIB in .Renviron [Y/n]

Dependencies

Step 4: The setup script is designed to guide you through the installation process and makes sure your enviroonment is setup correctly to run circtools. You will have to answer a few questions throughout this process:

We need to install two other programs of the Dieterich Lab circRNA suit, DCC and FUCHS, as well as R package dependencies for other modules of circtools
We'll install everything for you from GitHub and CRAN for you.

In order for the circtools primer design module to run, we need to install some R modules.
Please make sure R >= 3.3 is installed and your R library path is writeable .

Do you want to continue the automatic dependency installation?
-> "n" will only install the circtools base package
-> CTRL-C will abort the installation
 [Y/n]

Answer with “y” to automatically install CircTest, primex, DCC and FUCHS.

Finishing up

Step 5: Adding installation folder to $PATH. In order for circtools to find all exectuables, the setup will give you the possibility to add the folder /home/$USER/.local/bin/ automatically to your .bashrc file

In order for circtools to be globally callable, we would add the installation folder to the $PATH variable. Would you like us to do that?
Update $PATH in .bashrc? [Y/n]

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>]