{ "info": { "author": "Christopher DeBoever", "author_email": "cdeboever3@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "cdpipelines\n===========\n\nThis repository holds various bioinformatics pipelines.\n\nDependencies\n------------\n\nMany of the pipeline dependencies can be obtained using the ``prepare``\nsubmodule (see below). Additionally, a working Python environment is\nneeded along with some of the common scientific python packages. I\nrecommend using `Anaconda\npython `__ since it includes\nmost of the needed packages. If you are using Anaconda, I'd recommend\nmaking new environments for different projects. Besides the default\nAnaconda packages, you will need the following (available through\n``conda`` or ``pip``):\n\n- HTSeq\n- pandas\n- pysam (this is available through conda but currently it's an old\n version so you have to get it using ``pip``)\n- PyVCF\n\n``rpy2``\n~~~~~~~~\n\nInstalling ``rpy2`` can be tricky. Different versions of ``R`` and\n``rpy2`` don't work well together, so it's recommended to make a local\ninstallation of ``R`` using the ``prepare`` submodule and compile\n``rpy2`` against this installation. You can install ``R`` using\n``prepare.download_r`` and install ``rpy2`` using\n``prepare.download_install_rpy2``. ``prepare.download_install_rpy2``\nwill prompt you to set your PATH, LDFLAGS, and LD\\_LIBRARY\\_PATH to\ncorrectly install ``rpy2``. After installing ``rpy2``, you need to set\nyour PATH and LD\\_LIBRARY\\_PATH using these commands for every bash\nsession where you want to use this ``rpy2``. I'd recommend putting the\ncommands in a file that you source every time you load the project's\nAnaconda environment.\n\nSubmodules\n----------\n\n``general``\n~~~~~~~~~~~\n\n``general`` contains methods used in multiple pipelines. Some pipelines\nuse similar but different versions of some methods, so the pipelines\nwill have their own versions of those methods. Sometimes it may make\nsense to add options to a particular method that is used in multiple\npipelines (where each pipeline has slightly different versions) and add\nthe method into ``general``.\n\n``prepare``\n~~~~~~~~~~~\n\nThe ``prepare`` module contains functions for downloading various\nsoftware and reference files needed for the different pipelines.\n\n``rnaseq``\n~~~~~~~~~~\n\nThis pipeline currently starts from fastq files and has two steps. For\ndetailed information on each step, so the docstrings for each method.\nThe first step is ``align_and_sort`` which (optionally) removes\nduplicates, aligns the reads, and makes coverage bigwig files for use\nwith the UCSC genome browser or IGV. The read alignments are output in\nboth genomic and transcriptomic coordinates. The second step is\n``get_counts`` which counts reads overlapping genes for gene\ndifferential expression and exonic bins for use with DEXSeq.", "description_content_type": null, "docs_url": null, "download_url": "https://github.com/cdeboever3/cdpipelines/tarball/0.0.7", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/cdeboever3/cdpipelines", "keywords": "bioinformatics", "license": "MIT", "maintainer": null, "maintainer_email": null, "name": "cdpipelines", "package_url": "https://pypi.org/project/cdpipelines/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/cdpipelines/", "project_urls": { "Download": "https://github.com/cdeboever3/cdpipelines/tarball/0.0.7", "Homepage": "https://github.com/cdeboever3/cdpipelines" }, "release_url": "https://pypi.org/project/cdpipelines/0.0.7/", "requires_dist": null, "requires_python": null, "summary": "Various bioinformatics pipelines.", "version": "0.0.7" }, "last_serial": 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