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        "author": "Leonhard Wachutka",
        "author_email": "leonhard@wachutka.eu",
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        "description": "======\nwBuild\n======\n\n.. _user-overview:\n\nOverview\n--------\nwBuild is all about making your day easier resolving, updating and cascading various dependencies, pipeline rules and\ncode structs. The program lets you specify all the needed information in a YAML header right in your R code and let\nthe automated :code:`Snakemake` processes do the rest!\n\n\nYou can learn more about the features that wBuild provides either taking a look at the :ref:`features list <features>`\nor :ref:`looking at the HTML output of the demo project <running-demo>`. Another interesting thing to take a look at could be\nthe :ref:`installation requirements & procedure <installation>` and, in particular, :ref:`wBuild project tree structure <project-structure>`.\n\nYou can find functionality overview of wBuild and its relationship with Snakemake :ref:`here <overview-of-functionality>`.\n\nExample\n-------\n\nFirst, we :ref:`install <installation>` all the needed software requirements, including wBuild.\nThen, we :ref:`initialize wbuild <wbuild-init>` which creates :ref:`wBuild files <project-structure>` in our project.\n\nAfter that, we create an R script in the  and provide a :ref:`YAML header <yaml-headers>` with wBuild-supported tags:\n\n.. code-block:: R\n\n    #'---\n    #' title: Basic Input Demo\n    #' author: Leonhard Wachutka\n    #' wb:\n    #'  input:\n    #'  - iris: \"Data/{wbP}/iris.RDS\"\n    #'  output:\n    #'  - wBhtml: \"Output/html/030_AnalysisOfId_{id}.html\"\n    #'  type: noindex\n    #' output:\n    #'  html_document:\n    #'   code_folding: show\n    #'   code_download: TRUE\n    #'---\n\n    source('.wBuild/wBuildParser.R')\n    parseWBHeader(\"Scripts/Analysis1/050_PythonCode/030_AnalysisTemplate.R\")\n\n    id = snakemake@wildcards[[\"id\"]]\n    iris_df = wbReadRDS('iris')\n    colnames(iris_df) = gsub('\\\\.','',colnames(iris_df))\n    hist(iris_df[[id]],main=id)\n\nRunning :bash:`snakemake` now in the root directory of your project will now automatically\nparse the parameters out of scripts headers and create an HTML output showing the results of our petal analysis - found in HTML output directory\n(:code:`./Output/html` by default) along with a nice navigable HTML structure. Let's open one of the output HTML files, use the\nupper footer to navigate to the :ref:`needed subproject <scripts-structure>` (here *Analysis1*), and we will see a nicely rendered output of our\nscript:\n\n.. image:: /res/images/HTML_output_demo.png\n   :scale: 70%\n   :align: left\n\n|\n|\n\nYou can read more about :ref:`publishing the output HTML to your common server <publishing-the-output>` or try launching demonstration yourself as follows:\n\n.. _running-demo:\n\nRunning demo\n~~~~~~~~~~~~\n* Install wBuild. You can learn more about the installation process :ref:`here <installation>`.\n* Navigate to an *empty* directory.\n* Run :bash:`wbuild demo`. This will create a wBuild demo project with various examples.\n* Explore the files in :bash:`Scripts/`\n* Run :bash:`snakemake` on the root directory to let Snakemake do its thing (see below) and compile the project.\n* Open :code:`Output/html/index.html` in your web browser. From there, you can browse through sites showing and describing :ref:`basic features <features>` of wBuild on an example analysis.\n\n.. _overview-of-functionality:\n\nFunctionality & workflow\n------------------------\nwBuild is *not really a standalone application*, much more **a plugin and \"code generator\" for the later use of Snakemake**, which is *inevitable* part\nof a workflow involving wBuild: this way, you run :code:`snakemake` CLI each time you want to build and render your project!\n\nFirst, wBuild executes the initial, `setup` part of the workflow:\n\n.. image:: /res/images/snakemake_wbuild_diag_setup.jpg\n    :scale: 80%\n\n|\nAfter that comes the project build phase. During this step, snakemake with a help of wBuild does process your project and\ncreates the results. Following diagram shows the process:\n\n.. image:: /res/images/snakemake_wbuild_diag_build.jpg\n    :scale: 80%\n\n|\nAs you see, *Snakemake* actually takes the **main** role in a typical wBuild workflow, so every user is *encouraged* to\nlearn more about Snakemake - for instance `in its official documentation <http://snakemake.readthedocs.io/en/stable/>`_.\nYou are also welcome to take a look at the more :ref:`technial features <features>` that wBuild provides.\n\n\nA small overview of the functionality that wBuild provides:\n\n* wBuild enables reproducible research by appending every R-markdown script to the global analysis pipeline written in snakemake\n* All R scripts using R-markdown are compiled via knitr/Rmarkdown and rendered in a navigable web-page\n* This is achieved by writing the snakemake rules directly in the header of your R scripts\n* Headers allow the same flexibility (i.e. usage of python) as in the traditional Snakefile, but do not separate dependencies from the code where they are actually used.\n\n.. _project-structure:\n\nwBuild project structure\n------------------------\n\nAssert :code:`ROOT` is the root directory of your wBuild project.\n\nROOT/.wBuild\n    Is a directory with static wBuild files that *is not to be changed unless necessary*. There are all the\n    service files located.\n\nROOT/wbuild.yaml\n    It is a configuration file. Necessary but editable by the user. See :ref:`configuration file <configuration-file>`.\n\nROOT/.wBuild.depend\n    File *autogenerated* by wBuild. Contains rule information for the :ref:`Snakemake pipeline <overview-of-functionality>`.\n\n.. _scripts-structure:\n\nROOT/Scripts\n    Is a directory where all your scripts should be located within **subdirectories**. Organizing your code directly into subdirectories helps you to flexibly structure your project, to\n    present them divided by tabs in the HTML output or to\n    :ref:`apply the same script to the various equally structured data <script-mapping>`\n\nROOT/Output\n    Is a default output directory. 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