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            "Development Status :: 3 - Alpha",
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            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "RNAseq Analysis Pipeline\n========================\n\n|PyPI| |Build Status|\n\nInstallation\n------------\n\nInstall ``seqpipe`` using ``pip``:\n\n.. code:: bash\n\n    $ pip install seqpipe\n\n``seqpipe`` offers various commandline-arguments:\n\n::\n\n    $ seqpipe --help\n    Usage: seqpipe [OPTIONS] COMMAND [ARGS]...\n\n    Options:\n      --help  Show this message and exit.\n\n    Commands:\n      map\n      stats\n\nIn particular, the mapping pipeline is interesting:\n\n.. code:: bash\n\n    $ seqpipe map --help\n    Usage: seqpipe map [OPTIONS]\n\n    Options:\n      -r, --read PATH             Path to read file/directory.  [required]\n      -g, --genome PATH           Path to genome file/directory.  [required]\n      -o, --output DIRECTORY      Directory to save results to.\n      --scripts / --no-scripts    Whether to execute scripts or not.\n      -m, --min-read-len INTEGER  Minimal read length.\n      -M, --max-read-len INTEGER  Maximal read length.\n      -b, --bowtie-args TEXT      Extra arguments for bowtie.\n      -t, --threads INTEGER       How many threads to run in.\n      --help                      Show this message and exit.\n\nUsage\n-----\n\nTo map a directory of reads to two references, execute it as follows:\n\n.. code:: bash\n\n    $ seqpipe map \\\n      -r seqpipe/tests/data/reads/ \\\n      -g seqpipe/tests/data/references/10-ref.fa \\\n      -g seqpipe/tests/data/references/20-ref.fa \\\n      -o my_mapping\n\nThis will create a ``my_mapping`` directory which contains two\ndirectories: \\* ``runs`` stores all data related to each individual read\nfile \\* ``results`` contains data generated by scripts from the\n``scripts`` folder\n\nAn overview of the read distributions can then be generated via:\n\n.. code:: bash\n\n    $ seqpipe stats plot_rdist -o my_images/ my_mapping/\n\nExtras\n------\n\nAdditional useful scripts are contained in ``extra``. The entry point is\n``main.py`` (check ``python ./extra/main.py --help`` for help).\n\nThe respective individual files are: \\* ``sequential_pipeline.sh`` \\*\nmap length-filtered reads against multiple genomes in succession \\*\n``plot_sequential_data.py`` \\* visualize data obtained from sequential\npipeline \\* ``plot_expression_differences.py`` \\* visualize differences\nin RNAseq expression levels over pairs of samples\n\nLinks\n-----\n\n-  `Github <https://github.com/kpj/SeqPipe>`__\n-  `PyPi <https://pypi.python.org/pypi/seqpipe>`__\n\nDependencies\n------------\n\nTools: \\* cutadapt \\* fastqc \\* `more\ninfo <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/>`__\n\\* bowtie \\* samtools \\*\n`specifications <https://samtools.github.io/hts-specs/SAMv1.pdf>`__ \\*\nbedtools\n\nLanguages: \\* bash \\* python \\* numpy \\* pandas \\* seaborn \\* matplotlib\n\\* tqdm \\* biopython \\* pysam \\* joblib \\* click \\* sh \\* colorama\n\nDevelopment notes\n-----------------\n\nTests\n~~~~~\n\nRun tests using:\n\n.. code:: bash\n\n    $ tox\n\nRelease package\n~~~~~~~~~~~~~~~\n\nThis guide assumes a properly setup ``~/.pypirc``.\n\nBuild package:\n\n.. code:: bash\n\n    $ python setup.py sdist\n\nRegister it (only once):\n\n.. code:: bash\n\n    $ twine register dist/seqpipe-X.Y.Z.tar.gz\n\nTry installation locally:\n\n.. code:: bash\n\n    $ rm -rf /tmp/seqpipe_tmp\n    $ virtualenv /tmp/seqpipe_tmp\n    $ /tmp/seqpipe_tmp/bin/pip install dist/seqpipe-X.Y.Z.tar.gz\n    $ /tmp/seqpipe_tmp/bin/seqpipe --help\n\nTry installation using test-servers:\n\n.. code:: bash\n\n    $ twine upload -r test dist/seqpipe-X.Y.Z.tar.gz\n    $ pip install -i https://testpypi.python.org/pypi seqpipe\n    $ seqpipe --help\n\nCheck `testpypi-page <https://testpypi.python.org/pypi/seqpipe>`__.\n\nFinally, install it on actual server:\n\n.. code:: bash\n\n    $ twine upload dist/seqpipe-X.Y.Z.tar.gz\n    $ pip install -U seqpipe\n    $ seqpipe --help\n\nCheck actual `pypi-page <https://pypi.python.org/pypi/seqpipe>`__.\n\nMisc\n~~~~\n\nCreate dev-builds with:\n\n.. code:: bash\n\n    $ pip install --user -e .\n\nRun uninstalled version:\n\n.. code:: bash\n\n    $ python -m seqpipe.main\n\nEnable bash-autocompletion as follows:\n\n.. code:: bash\n\n    $ _SEQPIPE_COMPLETE=source seqpipe >> ~/.bashrc\n    $ . ~/.bashrc\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/seqpipe.svg?style=flat\n   :target: \n.. |Build Status| image:: https://travis-ci.org/kpj/SeqPipe.svg?branch=master\n   :target: https://travis-ci.org/kpj/SeqPipe",
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