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    "info": {
        "author": "Noah Hoffman",
        "author_email": "ngh2@uw.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: GNU General Public License (GPL)",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "===========\n TAXTASTIC\n===========\n\nTaxtastic is a python package used to build and maintain reference\npackages-- i.e. collections of reference trees, reference alignments,\nprofiles, and associated taxonomic information.\n\n.. image:: https://travis-ci.org/fhcrc/taxtastic.svg?branch=master\n    :target: https://travis-ci.org/fhcrc/taxtastic\n\nWe love it, but what is it?\n===========================\n\n* quickstart_\n* `full documentation`_\n\nA script named ``taxit`` provides a command line interface::\n\n  % taxit  --help\n  usage: taxit [-h] [-V] [-v] [-q]\n\t       {help,add_nodes,add_to_taxtable,check,composition,create,extract_nodes,findcompany,get_lineage,info,lonelynodes,new_database,refpkg_intersection,reroot,rollback,rollforward,rp,strip,taxids,taxtable,update,update_taxids}\n\t       ...\n\n  Creation, validation, and modification of reference packages for use with\n  `pplacer` and related software.\n\n  positional arguments:\n    {help,add_nodes,add_to_taxtable,check,composition,create,extract_nodes,findcompany,get_lineage,info,lonelynodes,new_database,refpkg_intersection,reroot,rollback,rollforward,rp,strip,taxids,taxtable,update,update_taxids}\n      help                Detailed help for actions using `help <action>`\n      add_nodes           Add nodes and names to a database\n      add_to_taxtable     Add nodes to an existing taxtable csv\n      check               Validate a reference package\n      composition         Show taxonomic composition of a reference package\n      create              Create a reference package\n      extract_nodes       Extract nodes from a given source in yaml format\n      findcompany         Find company for lonely nodes\n      get_lineage         Calculate the taxonomic lineage of a taxid\n      info                Show information about reference packages.\n      lonelynodes         Extracts tax ids of all lonely nodes in a taxtable\n      new_database        Download NCBI taxonomy and create a database\n      refpkg_intersection\n\t\t\t  Find the intersection of a taxtable and a refpkg's\n\t\t\t  taxonomy.\n      reroot              Taxonomically reroots a reference package\n      rollback            Undo an operation performed on a refpkg\n      rollforward         Restore a change to a refpkg immediately after being\n\t\t\t  reverted\n      rp                  Resolve path; get the path to a file in the reference\n\t\t\t  package\n      strip               Remove rollback and rollforward information from a\n\t\t\t  refpkg\n      taxids              Convert a list of taxonomic names into a recursive\n\t\t\t  list of species\n      taxtable            Create a tabular representation of taxonomic lineages\n      update              Add or modify files or metadata in a refpkg\n      update_taxids       Update obsolete tax_ids\n\n  optional arguments:\n    -h, --help            show this help message and exit\n    -V, --version         Print the version number and exit\n    -v, --verbose         Increase verbosity of screen output (eg, -v is\n\t\t\t  verbose, -vv more so)\n    -q, --quiet           Suppress output\n\n\n.. Targets ..\n.. _quickstart: http://fhcrc.github.com/taxtastic/quickstart.html\n.. _full documentation: http://fhcrc.github.com/taxtastic/index.html\n\n\nInstallation\n============\n\n``taxtastic`` requires Python versions 2.7 or 3.4+.  The simplest\nmethod of installing is using `pip <http://pip-installer.org>`_::\n\n  pip install taxtastic\n\nWe strongly recommend installation into a virtualenv. On a clean\nUbuntu 16.04 system, complete instructions for installing the\n``taxtastic`` package and the ``taxit`` command line entry point in a\nvirtualenv are below. Note that python2.7 is no longer installed\nby default in 16.04::\n\n  sudo apt-get update\n  sudo apt-get install python2.7 python-virtualenv\n\nOnce python2 is installed, create a virtualenv and install ``taxtastic``::\n\n  virtualenv taxtastic-env\n\nOr using python3.4+::\n\n  python3 -m venv taxtastic-env\n\nThen, for all python versions::\n\n  source taxtastic-env/bin/activate\n  pip install -U pip\n  pip install taxtastic\n\nIf you prefer to install from the git repository::\n\n  git clone https://github.com/fhcrc/taxtastic.git\n  cd taxtastic\n  virtualenv taxtastic-env  # eg, for python2\n  source taxtastic-env/bin/activate\n  pip install .\n\nIf you want to live dangerously and install the package to the system\ndespite our pleas not to do so::\n\n  sudo apt-get install python-pip\n  sudo pip install taxtastic\n\nIf you are not familiar with python virtual environments, the\nfollowing post is helpful:\nhttps://realpython.com/blog/python/python-virtual-environments-a-primer/\n\nFinally, ``taxit`` can be run from a docker image hosted from Docker\nHub (https://hub.docker.com/r/nghoffman/taxtastic/), for example::\n\n  docker run --rm -it -v $(pwd):$(pwd) -w $(pwd) nghoffman/taxtastic:0.8.3 taxit -v new_database\n\nNote that the tag for a given release must be specified: using\n``:latest`` (for this or any other Docker image) isn't very\nreproducible!\n\n\nsqlite3\n-------\n\nTaxtastic uses recursive common table expressions to query the\ntaxonomy database, which requires that the Python ``sqlite3`` module\nis built against sqlite3 library version of 3.8.3 or higher\n(http://www.sqlite.org/releaselog/3_8_3.html). You can check the\nversion like this::\n\n  python -c 'import sqlite3; print sqlite3.sqlite_version'\n\n``python setup.py`` will exit with an error if the sqlite3 library\ndependency is not met. On older systems (and for python2 only), it is\npossible to replace the builtin ``sqlite3`` module by installing\n``pysqlite2`` with updated sqlite3 libraries **before** installing the\npackage with pip using a provided script in the ``taxtastic`` git\nrepository (assuming an active virtualenv)::\n\n  dev/install_pysqlite.sh\n\nOr, to avoid cloning the repo::\n\n  curl https://raw.githubusercontent.com/fhcrc/taxtastic/master/dev/install_pysqlite.sh | bash\n\nAfter the script completes, confirm that ``pysqlite2`` was installed::\n\n  python -c 'from pysqlite2 import dbapi2; print dbapi2.sqlite_version'\n\nAt this point, taxtastic may be installed as described above.\n\nNote that ``pysqlite2`` is available for python2 only, so there really\nis no good option for using python3 on older systems like Ubuntu 14.04\nand earlier, unless you want to compile a version of the python3\ninterpreter linked against updated sqlite3 libraries. If you must use\nan older system, stick with python2, or use the Docker image.\n\nA note on databases\n===================\n\nThis project supports both sqlite3 and postgresql as database\nbackends. For most applications, we recommend sqlite3: some operations\n(particularly initial database creation) are much faster using sqlite3\ndue to the details of how postgresql enforces database constraints (we\nmay try to optimize this in the future - in theory, postgresql can be\nmade to be at least as fast). If you do want to use postgresql, note\nthat some of the queries consume a lot of memory, and the default\nconfiguration tends to be memory constrained (and this *really* slows\nthings down). On a reasonably new mac laptop, we found that the\noptimizations suggested here\n(http://big-elephants.com/2012-12/tuning-postgres-on-macos/) do the\ntrick.",
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