development/docker-demo/examples/HomePage_Example_2.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creation of a SoS workflow from interactive analysis"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Interactive data analysis"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Interactive data analysis can be performed in cells with different kernels as follows. Because SoS is an extension to Python 3, you can use arbitrary Python statements in SoS cells."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true,
    "kernel": "SoS"
   },
   "outputs": [],
   "source": [
    "fastq_file = 'raw_data.fastq'\n",
    "count_file = 'aligned.csv'\n",
    "output_pdf = 'myfigure.pdf'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "kernel": "Bash"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "count_reads --infile {fastq_file} --outfile {count_file}\n"
     ]
    }
   ],
   "source": [
    "%expand\n",
    "echo count_reads --infile {fastq_file} --outfile {count_file}\n",
    "echo \"A,B\" > {count_file}\n",
    "echo \"1,2\" >> {count_file}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "kernel": "R"
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<strong>pdf:</strong> 2"
      ],
      "text/latex": [
       "\\textbf{pdf:} 2"
      ],
      "text/markdown": [
       "**pdf:** 2"
      ],
      "text/plain": [
       "pdf \n",
       "  2 "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%expand\n",
    "count.data <- read.csv('{count_file}')\n",
    "pdf('{output_pdf}')\n",
    "plot(count.data)\n",
    "dev.off()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Conversion to a SoS Workflow"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "SoS workflows within a SoS Notebook are defined by sections marked by section headers (`[name: option]`). A `[global]` section should be used for definitions that will be used by all steps.\n",
    "\n",
    "You also need to convert scripts to SoS actions so that they can be executed as **complete** scripts. Remember also to change the cell type from subkernel to SoS."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "[global]\n",
    "fastq_file = 'raw_data.fastq'\n",
    "count_file = 'aligned.csv'\n",
    "output_pdf = 'myfigure.pdf'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "[analysis_10 (align)]\n",
    "sh: expand=True\n",
    "    echo count_reads --infile {fastq_file} --outfile {count_file}\n",
    "    echo \"A,B\" > {count_file}\n",
    "    echo \"1,2\" >> {count_file}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "[analysis_20 (plot)]\n",
    "R: expand=True\n",
    "    count.data <- read.csv('{count_file}')\n",
    "    pdf('{output_pdf}')\n",
    "    plot(count.data)\n",
    "    dev.off()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%preview --workflow"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%sosrun"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "SoS",
   "language": "sos",
   "name": "sos"
  },
  "language_info": {
   "codemirror_mode": "sos",
   "file_extension": ".sos",
   "mimetype": "text/x-sos",
   "name": "sos",
   "nbconvert_exporter": "sos_notebook.converter.SoS_Exporter",
   "pygments_lexer": "sos"
  },
  "sos": {
   "default_kernel": "SoS",
   "kernels": [
    [
     "Bash",
     "bash",
     "Bash",
     "#E6EEFF"
    ],
    [
     "R",
     "ir",
     "R",
     "#DCDCDA"
    ],
    [
     "SoS",
     "sos",
     "",
     ""
    ]
   ],
   "panel": {
    "displayed": true,
    "height": 0,
    "style": "side"
   },
   "version": "0.9.13.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}