{
    "info": {
        "author": "cwright",
        "author_email": "cwright@nanoporetech.com",
        "bugtrack_url": null,
        "classifiers": [],
        "description": "![Oxford Nanopore Technologies logo](https://github.com/nanoporetech/pomoxis/raw/master/images/ONT_logo_590x106.png)\n\nPomoxis - bioinformatics tools for nanopore research \n====================================================\n\n[![Build Status](https://travis-ci.org/nanoporetech/pomoxis.svg?branch=master)](https://travis-ci.org/nanoporetech/pomoxis)\n\nPomoxis comprises a set of basic bioinformatic tools tailored to nanopore\nsequencing. Notably tools are included for generating and analysing draft\nassemblies. Many of these tools are used by the research data analysis\ngroup at Oxford Nanopore Technologies.\n\nDocumentation can be found at https://nanoporetech.github.io/pomoxis/.\n\n\u00a9 2018 Oxford Nanopore Technologies Ltd.\n\nFeatures\n--------\n\n * Wraps third party tools with known good default parameters\n   and methods of use.\n * Creates an isolated environment with all third-party tools.\n * Can be installed with conda.\n * Streamlines common short analysis chains.\n * Includes a nanopore read simulator.\n * Server/client components for minimap2 and bwa.\n * Integrates into [katuali](https://github.com/nanoporetech/katuali)\n   for performing more complex analysis pipelines.\n * Open source (Mozilla Public License 2.0).\n\n\nCompatibility\n-------------\n\nPomoxis is developed on Ubuntu 16.04, other recent linuxes should be\nequally compatible (see build notes below). Pomoxis is known to work on\nat least some MacOS High Sierra configurations, though some components,\nnotably scrappy, are known to not work on some MacOS configurations\n(combinations of OS and xcode versions).\n\n\nInstallation\n------------\n\nMuch of pomoxis's functionality is dependent on thirty party tools. These\ncan be provided by the user, or can be installed with the help of the\nprovided `Makefile`\n\n**Installation with conda**\n\nPomoxis is available on [bioconda](https://bioconda.github.io/recipes/pomoxis/)\nand so can be most easily installed with:\n\n    conda install pomoxis\n\n**Installation with pip**\n  \nFor those who prefer python's native package manager, pomoxis is also available\non pypi and can be installed using pip:\n\n    pip install git+https://github.com/rrwick/Porechop\n    pip install pomoxis\n\nWe recommend using pomoxis within a virtual environment, viz.:\n\n    virtualenv pomoxis --python=python3 --prompt \"(pomoxis) \"\n    . pomoxis/bin/activate\n    pip install git+https://github.com/rrwick/Porechop\n    pip install pomoxis\n\nUsing this method requires the user to provide several binaries:\n\n * [minimap2](https://github.com/lh3/minimap2),\n * [miniasm](https://github.com/lh3/miniasm),\n * [racon](https://github.com/isovic/racon),\n * [samtools](https://github.com/samtools/samtools),\n * [bcftools](https://github.com/samtools/bcftools/), and\n * [seqkit](https://github.com/shenwei356/seqkit),\n\nand place these within the `PATH`.\n\n**Installation from source**\n\nWith this method pomoxis will install itself into a an isolated virtual\nenvironment. The installation will fetch, compile, and install all direct\ndependencies into the environment. Use this method if you do not wish to\nuse conda, but will not be providing the third-party binaries.\n\n> Before installing pomoxis is may be required to install some prerequisite\n> packages, best installed by a package manager. On Ubuntu these are:\n> * gcc-4.9\n> * g++-4.9\n> * zlib1g-dev\n> * libncurses5-dev\n> * python3-all-dev\n> * libhdf5-dev\n> * libatlas-base-dev\n> * libopenblas-base\n> * libopenblas-dev\n> * libbz2-dev\n> * liblzma-dev\n> * libffi-dev\n> * make\n> * python-virtualenv\n> * cmake (for racon)\n> * wget (for fetching modules from github)\n> * bzip2 (for extracting those modules)\n\nTo setup the environment run:\n\n    git clone --recursive https://github.com/nanoporetech/pomoxis\n    cd pomoxis\n    make install\n    . ./venv/bin/activate\n    \n\nThe installation of porechop (https://github.com/rrwick/Porechop)\nrequires a newer compiler than is a available on some systems. It may therefore\nbe necessary to install a newer compiler and set environment variables before\nthe `make install` step:\n\n    # For porechop to be compiled on older systems set these, e.g.:\n    export CXX=\"g++-4.9\" CC=\"gcc-4.9\"\n\nNote also that racon requires at least `gcc>=4.8.5` to\n[compile smoothly](https://github.com/isovic/racon/issues/57).\n\n\n**Installation without compiling third-party binaries**\n\nRunning the above within a pre-exisiting (virtual) environnment may well fail;\nadvanced may wish to simply run\n\n    python setup.py install\n\nin the standard manner after compiling the third party programs listed below\nand ensuring they are present on the `PATH`. The `setup.py` script can copy\nthe binaries into the python interpreter path if they are placed within a\ndirectory named `bincache` alongside `setup.py`. To make use of this facility\nrun:\n\n    pip install -r requirements.txt\n    POMO_BINARIES=1 python setup.py install\n\n\nThird party binaries\n--------------------\n\nThe distribution bundles some common bioinformatics tools:\n\n* miniasm\n* minimap2\n* racon\n* samtools\n* bcftools\n* seqkit\n* porechop\n\nHelp\n----\n\n**Licence and Copyright**\n\n\u00a9 2018 Oxford Nanopore Technologies Ltd.\n\n`pomoxis` is distributed under the terms of the Mozilla Public License 2.0.\n\n**Research Release**\n\nResearch releases are provided as technology demonstrators to provide early\naccess to features or stimulate Community development of tools. Support for\nthis software will be minimal and is only provided directly by the developers.\nFeature requests, improvements, and discussions are welcome and can be\nimplemented by forking and pull requests. However much as we would\nlike to rectify every issue and piece of feedback users may have, the \ndevelopers may have limited resource for support of this software. Research\nreleases may be unstable and subject to rapid iteration by Oxford Nanopore\nTechnologies.",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "",
        "keywords": "",
        "license": "",
        "maintainer": "",
        "maintainer_email": "",
        "name": "pomoxis",
        "package_url": "https://pypi.org/project/pomoxis/",
        "platform": "",
        "project_url": "https://pypi.org/project/pomoxis/",
        "project_urls": null,
        "release_url": "https://pypi.org/project/pomoxis/0.2.5/",
        "requires_dist": null,
        "requires_python": ">=3.5.2, <3.7",
        "summary": "Assembly, consensensus, and analysis tools by ONT research.",
        "version": "0.2.5"
    },
    "last_serial": 5917679,
    "releases": {
        "0.2.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "11a6ee823170de262ba4272eb50eea49",
                    "sha256": "4001024e7c2b200e4924c2924f3c423e3f7464b51501619b3c310f51b5120df9"
                },
                "downloads": -1,
                "filename": "pomoxis-0.2.2.tar.gz",
                "has_sig": false,
                "md5_digest": "11a6ee823170de262ba4272eb50eea49",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.5.2, <3.7",
                "size": 89163,
                "upload_time": "2019-02-22T17:51:40",
                "url": "https://files.pythonhosted.org/packages/45/15/4b49595826cc4975e73952c5416a72c994477a5e7b099976577d88f105df/pomoxis-0.2.2.tar.gz"
            }
        ],
        "0.2.2a1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "ac864d4e6ce248b0e321aa3d5906dae4",
                    "sha256": "62f5121020ce00f056714240d50d580d0c23a64d502a80ea529d431655367e88"
                },
                "downloads": -1,
                "filename": "pomoxis-0.2.2a1.tar.gz",
                "has_sig": false,
                "md5_digest": "ac864d4e6ce248b0e321aa3d5906dae4",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.5.2, <3.7",
                "size": 46234,
                "upload_time": "2019-02-22T16:24:38",
                "url": "https://files.pythonhosted.org/packages/c0/59/a56134534e8982b057c383eb347cf395305c28c3fcd47e42ca3866401212/pomoxis-0.2.2a1.tar.gz"
            }
        ],
        "0.2.2a2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "bcf389a6510b1bd6719ff152d23220ad",
                    "sha256": "cfed0307424929a9bb1e44f6acd2e1d8b5741532581ae38ce510d565979247c6"
                },
                "downloads": -1,
                "filename": "pomoxis-0.2.2a2.tar.gz",
                "has_sig": false,
                "md5_digest": "bcf389a6510b1bd6719ff152d23220ad",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.5.2, <3.7",
                "size": 89085,
                "upload_time": "2019-02-22T16:57:32",
                "url": "https://files.pythonhosted.org/packages/7f/90/ed673752a756a3477dcc242f938c46aa7fabd7e9a061438a8606c3a99e6e/pomoxis-0.2.2a2.tar.gz"
            }
        ],
        "0.2.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "beae8a551a725febac36dcbd7e73e6af",
                    "sha256": "e87e632ca3ef172590e059ddb7282d933294439ef71c3df67d9b56a969a45b8d"
                },
                "downloads": -1,
                "filename": "pomoxis-0.2.3.tar.gz",
                "has_sig": false,
                "md5_digest": "beae8a551a725febac36dcbd7e73e6af",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.5.2, <3.7",
                "size": 7058539,
                "upload_time": "2019-07-10T10:28:37",
                "url": "https://files.pythonhosted.org/packages/79/63/59892ab3f851f6088ba6c5f97fc1e871cbf6ce6e310b8da1e54d4d1427c1/pomoxis-0.2.3.tar.gz"
            }
        ],
        "0.2.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "318bf652a9c1817dc946753ced564d7a",
                    "sha256": "2f4a45d1bc48725a24ede76b07cd66bb9432e0b382685f4ea0abc4715eb96fc2"
                },
                "downloads": -1,
                "filename": "pomoxis-0.2.4.tar.gz",
                "has_sig": false,
                "md5_digest": "318bf652a9c1817dc946753ced564d7a",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.5.2, <3.7",
                "size": 89256,
                "upload_time": "2019-09-24T11:15:02",
                "url": "https://files.pythonhosted.org/packages/fa/d1/392448c751e2c024e51075f04d81067530d326e33a36dd6726f617bb3b4d/pomoxis-0.2.4.tar.gz"
            }
        ],
        "0.2.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b932863fc4530ba6b1e4b03cff613273",
                    "sha256": "014894e06e107701593d2d470785f9ac940a6907a456cae1b2e65447f0bcf2e9"
                },
                "downloads": -1,
                "filename": "pomoxis-0.2.5.tar.gz",
                "has_sig": false,
                "md5_digest": "b932863fc4530ba6b1e4b03cff613273",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.5.2, <3.7",
                "size": 89319,
                "upload_time": "2019-10-02T12:34:27",
                "url": "https://files.pythonhosted.org/packages/2d/53/aac67c49cd9c3e371dfe4ae88674d68271e8d5eb3d53111edb4c44efa4d0/pomoxis-0.2.5.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "b932863fc4530ba6b1e4b03cff613273",
                "sha256": "014894e06e107701593d2d470785f9ac940a6907a456cae1b2e65447f0bcf2e9"
            },
            "downloads": -1,
            "filename": "pomoxis-0.2.5.tar.gz",
            "has_sig": false,
            "md5_digest": "b932863fc4530ba6b1e4b03cff613273",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.5.2, <3.7",
            "size": 89319,
            "upload_time": "2019-10-02T12:34:27",
            "url": "https://files.pythonhosted.org/packages/2d/53/aac67c49cd9c3e371dfe4ae88674d68271e8d5eb3d53111edb4c44efa4d0/pomoxis-0.2.5.tar.gz"
        }
    ]
}