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SCReadCounts

SCReadCounts Installation

SCReadCounts 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 pythonic version requires pysam, numpy and scipy along with other packages (See the install instructions for more details). Conda-based installation of Python source provides a simple, platform-independent installation and update procedure.

Binary Package Installation

64-bit Linux

  1. Unpack the download. 
     % tar xzf SCReadCounts-*.Linux-x86_64.tgz
 % cd SCReadCounts-*.Linux-x86_64
  2. See the graphical user interface. 
     % bin/scReadCounts
  3. Command-line help. 
     % bin/scReadCounts -h
  4. Run the examples. 
     % cd data
 % ./example.sh

Intel-based MacOS

  1. Unpack the download. 
     % tar xzf SCReadCounts-*.Darwin-x86_64.tgz
 % cd SCReadCounts-*.Darwin-x86_64.tgz
  2. See the graphical user interface. 
     % bin/scReadCounts
  3. Command-line help. 
     % bin/scReadCounts -h
  4. 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 screadcounts
  3. Run scReadCounts: 
     % conda run -n HorvathLab --live-stream scReadCounts
  4. Command-line help: 
     % conda run -n HorvathLab --live-stream scReadCounts -h
  5. Update scReadCounts to latest version: 
     % conda update -n HorvathLab -c bioconda screadcounts

Python Source Installation

  1. Unpack the downloaded: 
     % tar xzf SCReadCounts-*.Python-3.7.tgz
 % cd SCReadCounts-*.Python-3.7.tgz
  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/scReadCounts
  5. Command-line help. 
     % bin/scReadCounts -h
  6. Run the examples. 
     % cd data
 % ./example.sh

See Also

SCReadCounts Home, Usage, Input Files, Output Files