ReadCounts Installation

ReadCounts is available as a self-contained binary package for 64-bit Linux and MacOS systems and as Python source. The self-contained binary package is appropriate for most Linux and MacOS users. The pysam package, plus a variety of common third-party python packages including numpy and scipy must be installed to use ReadCounts in Python source form. See the install instructions below for more details.

Binary Package Installation

Linux

1. Unpack the download.

    tar xzf ReadCounts-*.Linux-x86_64.tgz
    cd ReadCounts-*.Linux-x86_64
   

2. See the graphical user interface.

    bin/readCounts
   

3. Command-line help.

    bin/readCounts -h
   

4. Run the examples.

    cd data
    ./example.sh
   

   MacOS

5. Unpack the download.

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

6. See the graphical user interface.

    % bin/readCounts
   

7. Command-line help.

    % bin/readCounts -h
   

8. Run the examples.

    % cd data
    % ./example.sh
   

Python Source Installation

1. Unpack the downloaded:

    tar xzf ReadCounts-*.Python-3.7.tgz
    cd ReadCounts-*.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/readCounts
   

5. Command-line help.

    bin/readCounts -h
   

6. Run the examples.

    cd data
    ./example.sh
   

See Also

ReadCounts Home, Usage, Input Files, Output Files