SCExecute Installation

SCExecute is available as a self-contained binary package for 64-bit Intel-based Linux and MacOS (Darwin), and as Python Source. The self-contained binary packages are appropriate for most users. The pysam package, plus a variety of common third-party python packages including numpy and scipy must be installed to use SCExecute in Python source form. See the install instructions below for more details. Conda-based installation of Python source provides a simple, platform-independent installation and update procedure.

• Binary Package Installation
  • 64-bit Linux
  • Intel-based MacOS
• Conda-based Installation
• Python Source Installation

Binary Package Installation

64-bit Linux

1. Unpack the download.

    % tar xzf SCExecute-*.Linux-x86_64.tgz
    % cd SCExecute-*.Linux-x86_64
   

2. See the graphical user interface.

    % bin/scExecute
   

3. Command-line help.

    % bin/scExecute -h
   

4. Run the examples.

    % cd data
    % ./example.sh
   

   Intel-based MacOS

5. Unpack the download.

    % tar xzf SCExecute-*.Darwin-x86_64.tgz
    % cd SCExecute-*.Darwin-x86_64
   

6. See the graphical user interface.

    % bin/scExecute
   

7. Command-line help.

    % bin/scExecute -h
   

8. Run the examples.

    % cd data
    % ./example.sh
   

Conda-based Installation

1. Create a conda environment for HorvathLab tools (if not done previously)

    % conda create -n HorvathLab
   

2. Install in the conda environment

    % conda install -n HorvathLab -c bioconda scexecute
   

3. Run scExecute:

    % conda run -n HorvathLab --live-stream scExecute
   

4. Command-line help:

    % conda run -n HorvathLab --live-stream scExecute -h
   

5. Update scExecute to latest version:

    % conda update -n HorvathLab -c bioconda scexecute
   

Python Source Installation

1. Unpack the downloaded:

    % tar xzf SCExecute-*.Python-3.7.tgz
    % cd SCExecute-*.Python-3.7
   

2. Install the necessary, and optional (if desired), Python 3 packages:

    % pip3 install -r src/requirements.txt 
    % pip3 install -r src/optional_requirements.txt
   

3. If python3 is not on your path or is called something else

    % export PYTHON3=<path to python3>
   

   or

    % setenv PYTHON3 <path to python3>
   

4. See the graphical user interface (if wxPython is installed).

    % bin/scExecute
   

5. Command-line help.

    % bin/scExecute -h
   

6. Run the examples.

    % cd data
    % ./example.sh
   

See Also

SCExecute Home, Usage, Input Files, Cell Barcodes, Command/Template Substitution, Examples