### Install Reference Genome (wget default) Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Install reference genome files for SigProfilerMatrixGenerator using the 'install' function. This example installs 'GRCh37' and uses bash commands by default. ```python >> from SigProfilerMatrixGenerator import install as genInstall >> genInstall.install('GRCh37', bash=True) ``` -------------------------------- ### Install SigProfilerMatrixGenerator Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Install the SigProfilerMatrixGenerator tool using pip. This command should be run after ensuring Python and pip are correctly installed and configured. ```bash $ pip install SigProfilerMatrixGenerator ``` -------------------------------- ### Install SigProfilerMatrixGenerator Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Install the SigProfilerMatrixGenerator tool using pip. This command should be run after all prerequisites are met. ```bash $ pip install SigProfilerMatrixGenerator ``` -------------------------------- ### Install Reference Genome Source: https://osf.io/s93d5/wiki/6.%20Quick%20Start%20Example Download and install a specific reference genome assembly for use with the tool. ```python $ python3 >> from SigProfilerMatrixGenerator import install as genInstall >> genInstall.install('GRCh37') ``` -------------------------------- ### Install SigProfilerMatrixGenerator Source: https://osf.io/s93d5/wiki Install the SigProfilerMatrixGenerator tool using pip. This command should be run after all prerequisites are met. ```bash pip install SigProfilerMatrixGenerator ``` -------------------------------- ### Install Reference Genome (rsync alternative) Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Install reference genome files using the 'rsync' parameter set to True as an alternative to wget, which may be necessary if firewalls are in place. ```python >> from SigProfilerMatrixGenerator import install as genInstall >> genInstall.install('GRCh37', rsync=False) ``` -------------------------------- ### Install Reference Genomes Source: https://osf.io/s93d5/wiki Python commands to install reference genome files for SigProfilerMatrixGenerator, including an alternative for firewall-restricted environments. ```python $ python3 >> from SigProfilerMatrixGenerator import install as genInstall >> genInstall.install('GRCh37', bash=True) ``` ```python $ python3 >> from SigProfilerMatrixGenerator import install as genInstall >> genInstall.install('GRCh37', rsync=False) ``` -------------------------------- ### Check Installed Modules Source: https://osf.io/s93d5/wiki/6.%20Quick%20Start%20Example Verify that SigProfilerMatrixGenerator is present in the list of installed Python modules. ```python $python Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 26 2016, 10:47:25) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> help("modules") Please wait a moment while I gather a list of all available modules... IN argparse setuptools SigProfilerMatrixGenerator ... ``` -------------------------------- ### Check Pip Version Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Verify the installed pip version and its associated Python installation. This is useful when multiple Python versions are present. ```bash $ pip --version ``` ```bash $ pip --version pip 19.0.1 from c:\users\name\appdata\local\programs\python\pythonversion\lib\site-packages\pip ``` -------------------------------- ### Check Pip Version Source: https://osf.io/s93d5/wiki Confirm the installed version of pip and its associated Python version. This is useful for managing multiple Python installations. ```bash $ pip --version ``` ```bash $ pip --version pip 19.0.1 from /Library/Frameworks/SomeFilePath/ ``` -------------------------------- ### Check Python Version Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Verify the installed Python version on Windows systems. If multiple versions are present, use 'python3 --version'. ```bash > python --version ``` ```bash > python3 --version Python 3.7.3 ``` -------------------------------- ### Check Pip Version Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Confirm the installed pip version and its associated Python installation. This helps in managing packages for different Python environments. ```bash $ pip --version ``` -------------------------------- ### Add Python to PATH Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Add the Python installation directory to the system's PATH environmental variable if Python is not recognized. Replace '[path_to_python were .exe file is]' with the actual path. ```bash $ setx PATH "%PATH%"; [path_to_python were .exe file is]" ``` -------------------------------- ### Check Python Version Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Verify the installed Python version in Terminal. This command is useful for ensuring compatibility with SigProfilerMatrixGenerator. ```bash $ python --version ``` ```bash $ python3 --version ``` -------------------------------- ### Check Python Version Source: https://osf.io/s93d5/wiki Verify if the required Python version (3.4+) is installed on your system. This command is run in the Terminal or Command Line. ```bash $ python --version ``` ```bash $ python3 --version Python 3.7.3 ``` -------------------------------- ### Verify Python Environment Source: https://osf.io/s93d5/wiki/6.%20Quick%20Start%20Example Check the active Python version in the terminal to ensure it is Python 3. ```bash $python Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 26 2016, 10:47:25) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information. >> ``` -------------------------------- ### Troubleshoot Python Command Source: https://osf.io/s93d5/wiki Error message encountered when Python is not in the system PATH and the command to fix it. ```bash > python 'python' is not recognized as an internal or external command ``` ```bash $ setx PATH "%PATH%"; [path_to_python were .exe file is]" ``` -------------------------------- ### Upgrade SigProfilerMatrixGenerator Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Upgrade SigProfilerMatrixGenerator to the latest version using pip. Run this command in Terminal or the Command Line. ```bash pip install SigProfilerMatrixGenerator --upgrade ``` -------------------------------- ### Add Pip to PATH Source: https://osf.io/s93d5/wiki/1.%20Installation%20-%20Python Add the pip Scripts directory to the system's PATH environmental variable if pip is not recognized. Replace '[path_to_python + \Scripts\]' with the actual path. ```bash $ setx PATH "%PATH%"; [path_to_python + \Scripts\]" ``` -------------------------------- ### Troubleshoot pip Command Source: https://osf.io/s93d5/wiki Error message encountered when pip is not in the system PATH and the command to fix it. ```bash $ pip 'pip' is not recognized as an internal or external command ``` ```bash $ setx PATH "%PATH%"; [path_to_python + \Scripts\]" ``` -------------------------------- ### Generate Matrices Source: https://osf.io/s93d5/wiki/6.%20Quick%20Start%20Example Execute the matrix generation function within a Python session using the project name, reference genome, and input path. ```python $ python3 >>from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen >>matrices = matGen.SigProfilerMatrixGeneratorFunc("test", "GRCh37", "/Users/ebergstr/Desktop/test",plot=True) ``` -------------------------------- ### Upgrade SigProfilerMatrixGenerator Source: https://osf.io/s93d5/wiki Update the SigProfilerMatrixGenerator tool to the latest version using pip. Run this command in Terminal or the Command Line. ```bash pip install SigProfilerMatrixGenerator --upgrade ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.