To update the development version, use: pip install -force git+ Updating MultiQCĪt any time by running the following command: pip install -upgrade multiqc Note that it is not recommended to use the command python setup.py installĪs this has been superseded by pip and does not correctly handle some package Git not installed? No problem - just download the flat files: curl -LOk If you'd rather not use either of these tools, you can clone the code and install the code yourself: git clone pip install -user multiqc Manual installation To use virtual environments, as described above). Your home directory with the -user parameter (though it's probably better Note that if you have problems with read-only directories, you can install to If you would like the development version, the command is: pip install git+ Otherwise you can find installation instructions here. It comes bundled with recent versions of Python, This is the easiest way to install MultiQC. Please see the Bioconda documentation for more details. If you're using conda as described above, you can install MultiQC from the biocondaĬhannel as follows: conda install -c bioconda -c conda-forge multiqc That the environment is loaded every time you load the terminal. You'll want to add the conda activate p圓.7 line to your. Once conda is installed, you can create a Python environment with the following commands: conda create -name p圓.7 python=3.7 You can installation instructions for Miniconda Our favourite is conda, a cross-platform tool to manage Python environments. We recommend using virtual environments to manage your Python installation. MultiQC needs Python version 2.7+, 3.4+ or 3.5+. To see if you have python installed, run python -version on the command line. Step back and think about Python virtual environments / conda instead (see below). If you find yourself prepending sudo to any MultiQC commands, take a This often causes problems and it's a little risky to mess Installing MultiQC System Pythonīefore we start - a quick note that using the system-wide installation of Python It also saves a directory of dataįiles with all parsed data for further downstream use. Generates a single stand-alone HTML report file. It parses relevant information from these and When you launch MultiQC, it recursively searches through any provided file pathsĪnd finds files that it recognises.

It's designed to be placed at the end of analysis pipelines or to be run manually MultiQC doesn't run other tools for you.

MultiQC is a reporting tool that parses summary statistics from results and log files

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