Setup and Install Velocyto
Requirements
To run VeloCyto, you will need Python >=3.6.0 (we have no plans to support python<=3.5). We recommend using anaconda and the conda command to install dependencies
cd $HOME/opt
wget https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh
bash Anaconda3-2019.10-Linux-x86_64.sh
Accept all defaults for “Do you wish the installer to initialize Anaconda3 by running conda init?” say Yes.
Verify that conda is installed by running it in the Terminal:
conda update -- all and conda upgrade --all
Samtools
Building and installing
cd $HOME/opt
wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
tar jxvf samtools-1.10.tar.bz2
cd $HOME/opt/samtools-1.10
./configure --prefix=$HOME/opt/samtools
make
make install
export PATH=$HOME/opt/samtools/bin:$PATH
Run the following command to make sure you have all the dependencies correctly installed:
conda install numpy scipy cython numba matplotlib scikit-learn h5py click
If there are issues with conda try running it in the Terminal:
pip install velocyto
Verify the installation by running in the Terminal:
velocyto --help
Usage: velocyto [OPTIONS] COMMAND [ARGS]…
Options:
–version Show the version and exit.
–help Show this message and exit.
Commands:
run Runs the velocity analysis outputting a loom file
run10x Runs the velocity analysis for a Chromium Sample
run-dropest Runs the velocity analysis on DropEst preprocessed data
run-smartseq2 Runs the velocity analysis on SmartSeq2 data (independent bam file per cell)
tools helper tools for velocyto