Get started: Download CASPR Code and Data
CASPR is being developed and tested under Linux and macOS.
In order to use it, first you need to clone the repository:
git clone https://github.com/judithbergada/CASPR.git $HOME/CASPR
For a proper installation, it is also recommended to run:
# Add CASPR to your PATH echo "export PATH=$HOME/CASPR/source:$PATH" >> $HOME/.bashrc source $HOME/.bashrc # Please, note that the previous commands do not work if you use Zsh
At this point, the tool should be available in your computer. You can check it:
Conda Environment Installation
CASPR employs several software packages to carry out its different functions:
Once Miniconda is installed, you can obtain the required packages by executing the following commands on your terminal:
# Create environment conda create -n caspr --yes python=3.5 # Install required software conda install -n caspr --yes r=3.5.0 conda install -n caspr -c bioconda --yes cutadapt conda install -n caspr -c bioconda --yes star conda install -n caspr -c bioconda --yes bbmap conda install -n caspr -c bioconda --yes samtools=1.4 conda install -n caspr -c bioconda --yes mageck conda install -n caspr -c bioconda --yes vispr conda install -n caspr -c bioconda --yes fastqc conda install -n caspr -c conda-forge --yes ghostscript conda install -n caspr -c conda-forge --yes openjdk
Installation on macOS
Since macOS uses custom versions of
grep, it is also necessary to
install the latest GNU version to run CASPR. For that, first you need to
Once HomeBrew works at your device, you only need to copy the following commands on your terminal:
# Install sed and grep brew install gnu-sed grep # Make sure the installed versions are the first ones available in your PATH echo "export PATH=\"/usr/local/opt/gnu-sed/libexec/gnubin:\$PATH\"" >> ~/.bashrc echo "export PATH=\"/usr/local/opt/grep/libexec/gnubin:\$PATH\"" >> ~/.bashrc source ~/.bashrc
Now, you can start using CASPR on Linux or macOS!
To use the tool, please do not forget to activate the Conda Environment!
# Activate for Linux source activate caspr # Activate for macOS conda activate caspr
Users of IBU cluster
Users of IBU cluster (Interfaculty Bioinformatics Unit, University of Bern) do not need to follow the guide to install a Conda Environment.
Instead, you can load the required software packages, which are all installed in the cluster. This can be done as follows:
# Import software: only for users of IBY cluster module add UHTS/Analysis/fastx_toolkit/0.0.13.2 module add UHTS/Aligner/STAR/2.6.0c module add UHTS/Analysis/samtools/1.4 module add R/3.5.1 module add UHTS/Quality_control/mageck-vispr/0.5.4