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Facility\n(BCF) at the University of Manchester (UoM).\n\nFull documentation is available at https://auto-process-ngs.readthedocs.io.\n\nOverview\n********\n\nThis package provides a small set of utilities to generate FASTQ files from\nraw ``bcl`` files output by Illumina MiSEQ and HiSEQ sequencers, and to\nperform other task such as QC runs and file management.\n\nIt also facilitates handling problem situations such as barcoding issues or\nincomplete runs.\n\nInstallation\n************\n\nIt is recommended to use::\n\n    pip install .\n\nfrom within the top-level source directory to install the package.\n\nTo use the package without installing it first you will need to add the\ndirectory to your ``PYTHONPATH`` environment.\n\nTo install directly from github using ``pip``::\n\n    pip install git+https://github.com/fls-bioinformatics-core/auto_process_ngs.git\n\n**Note**\n\n* For pip 1.5: you will need to specify the ``--process-dependency-links``\n  argument to the ``install`` command to pull in the dependencies.\n* For pip 1.6: you must first do ``pip install -r requirements.txt`` to\n  pull in the dependencies.\n\nDocumentation\n*************\n\nDocumentation based on ``sphinx`` is available under the ``docs`` directory.\n\nTo build::\n\n    cd docs\n    make html\n\nwhich creates the documentation in the ``docs/build`` subdirectory.\n\nRunning Tests\n*************\n\nThe tests can be run using::\n\n    python setup.py test\n\nIn addition the tests are run via GitHub Actions whenever the repository\nis updated:\n\n.. image:: https://github.com/fls-bioinformatics-core/auto_process_ngs/workflows/Python%20CI/badge.svg\n   :target: https://github.com/fls-bioinformatics-core/auto_process_ngs/actions?query=workflow%3A%22Python+CI%22\n\nDependencies\n************\n\nThe package depends on the ``genomics-bcftbx`` package, available from\nhttps://github.com/fls-bioinformatics-core/genomics\n\nDevelopmental version\n*********************\n\nThe developmental branch of the code on github is ``devel``, this can be\ninstalled using::\n\n    pip install git+https://github.com/fls-bioinformatics-core/auto_process_ngs.git@devel\n\nUse the ``-e`` option to install an 'editable' version (see the section on\n`\"Editable\" installs \u003chttps://pip.pypa.io/en/latest/reference/pip_install.html#editable-installs\u003e`_\nin the pip documentation).\n\nContributing\n************\n\nSee `CONTRIBUTING.md \u003cCONTRIBUTING.md\u003e`_ file for guidelines on how to\ncontribute to the project.","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffls-bioinformatics-core%2Fauto_process_ngs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffls-bioinformatics-core%2Fauto_process_ngs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffls-bioinformatics-core%2Fauto_process_ngs/lists"}