Intro to Linux added

notebooks/Introduction to Linux.ipynb

@@ -0,0 +1,239 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# History of Linux\n",
+    " ## Linux was developed by Linus Torvalds, a computer science student at University of Helsinki. \n",
+    " He wanted to make a freely available version of # Hist UNIX for home users as UNIX was only available at Universities or Offices. So he developed LINUX. (http://www.tldp.org/LDP/intro-linux/html/sect_01_03.html)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Common Linux commands-\n",
+    "\n",
+    "cd /directorypath\tChange to directory.\n",
+    "\n",
+    "clear\tClear a command line screen/window for a fresh start.\n",
+    "\n",
+    "cp [options] source destination\tCopy files and directories.\n",
+    "\n",
+    "date [options]\tDisplay or set the system date and time.\n",
+    "\n",
+    "file [options] filename\tDetermine what type of data is within a file.\n",
+    "\n",
+    "find [pathname] [expression]\tSearch for files matching a provided pattern.\n",
+    "\n",
+    "grep [options] pattern [filesname]\tSearch files or output for a particular pattern.\n",
+    "\n",
+    "less [options] [filename]\tView the contents of a file one page at a time.\n",
+    "\n",
+    "ls [options]\tList directory contents.\n",
+    "\n",
+    "man [command]\tDisplay the help information for the specified command.\n",
+    "\n",
+    "mkdir [options] directory\tCreate a new directory.\n",
+    "\n",
+    "mv [options] source destination\tRename or move file(s) or directories.\n",
+    "\n",
+    "pwd\tDisplay the pathname for the current directory.\n",
+    "\n",
+    "rm [options] directory\tRemove (delete) file(s) and/or directories.\n",
+    "\n",
+    "rmdir [options] directory\tDelete empty directories.\n",
+    "\n",
+    "tail [options] [filename]\tDisplay the last n lines of a file (the default is 10).\n",
+    "\n",
+    "head [options] [filenname]  Displays the first n lines of a file (the default is 10)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Now lets use some of these commands on our phage data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 1. ls command lists the content of the directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " Volume in drive C is Windows\n",
+      " Volume Serial Number is 0EDB-005C\n",
+      "\n",
+      " Directory of C:\\Users\\Jigyasa\\phage-lab-master\\notebooks\n",
+      "\n",
+      "2016-08-25  04:14 PM    <DIR>          .\n",
+      "2016-08-25  04:14 PM    <DIR>          ..\n",
+      "2016-08-25  04:11 PM    <DIR>          .ipynb_checkpoints\n",
+      "2016-08-22  06:59 PM            10,802 1. Raw data.ipynb\n",
+      "2016-08-25  04:14 PM             2,542 Introduction to Linux.ipynb\n",
+      "2016-08-22  06:59 PM    <DIR>          reads\n",
+      "               2 File(s)         13,344 bytes\n",
+      "               4 Dir(s)  133,559,926,784 bytes free\n"
+     ]
+    }
+   ],
+   "source": [
+    "ls"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 2. pwd displays the pathname of the current working directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "u'C:\\\\Users\\\\Jigyasa\\\\phage-lab-master\\\\notebooks'"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pwd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 3. cd helps to change the current directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "C:\\Users\\Jigyasa\\phage-lab-master\\notebooks\\reads\n"
+     ]
+    }
+   ],
+   "source": [
+    "cd reads"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 4. cd .. takes you back to parent directory which is \"notebooks\" in this case.\n",
+    "### You can also use cd / which takes you to the root directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "C:\\Users\\Jigyasa\\phage-lab-master\\notebooks\n"
+     ]
+    }
+   ],
+   "source": [
+    "cd .."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 5. ls -lh lists the files in long format with readable file size\n",
+    "### ./ command lets you run a file in current directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "'ls' is not recognized as an internal or external command,\n",
+      "operable program or batch file.\n"
+     ]
+    }
+   ],
+   "source": [
+    "!ls -lh ./reads"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
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+}