slides/02-20201008.ipynb

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   "source": [
    "# Chapter 1 - Unix\n",
    "\n",
    "![](img/terminal.png)"
   ]
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    "![](img/legodog1.jpg)"
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   "source": [
    "# Today\n",
    "- How did you manage with Chapter 1?\n",
    "- What was difficult?\n",
    "- How did you solve it?"
   ]
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    "# Common issues when learning Unix\n",
    "\n",
    "1. Absolute or relative paths\n",
    "2. The root directory\n",
    "3. The `$PATH` variable\n",
    "4. File permissions\n",
    "5. Redirection and piping of STDIN, STDERR and STDOUT"
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   "source": [
    "# Absolute or relative paths\n",
    "\n",
    "```\n",
    "cd /home/nylander/tmp\n",
    "cd tmp\n",
    "```"
   ]
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    "# The root directory\n",
    "\n",
    "```\n",
    "cd tmp\n",
    "cd /tmp\n",
    "```"
   ]
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   "source": [
    "# The `PATH` variable\n",
    "\n",
    "\"command not found\"\n",
    "\n",
    "```\n",
    "echo $PATH\n",
    "```"
   ]
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    "# File permissions\n",
    "\n",
    "\"Permission denied\"\n",
    "\n",
    "```\n",
    "ls -l foo\n",
    "chmod +x foo\n",
    "ls -l foo\n",
    "```\n"
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   "source": [
    "# Redirection and piping of STDIN, STDERR and STDOUT\n",
    "\n",
    "```\n",
    "program file > out.txt 2> log.txt\n",
    "```"
   ]
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   "source": [
    "# Redirection and piping of STDIN, STDERR and STDOUT\n",
    "\n",
    "![](img/std1.png)"
   ]
  },
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   "source": [
    "# Redirection and piping of STDIN, STDERR and STDOUT\n",
    "\n",
    "![](img/std2.png)"
   ]
  },
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   "source": [
    "# Redirection and piping of STDIN, STDERR and STDOUT\n",
    "\n",
    "![](img/std3.png)"
   ]
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   "source": [
    "# Redirection and piping of STDIN, STDERR and STDOUT\n",
    "\n",
    "```\n",
    "program file > stdout.txt 2> stderr.txt\n",
    "\n",
    "program file 1> stdout.txt 2> stderr.txt\n",
    "\n",
    "program < input > stdout.txt\n",
    "\n",
    "program1 file | program2 > out.txt\n",
    "```"
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   "source": [
    "# Assignment for next occasion (Oct 15)\n",
    "\n",
    "- Chapter 2. Version control (using `git`)\n",
    "\n",
    "- **Exercises in** [notebooks/2-version-control.ipynb](https://github.com/Naturhistoriska/BIOinfo-course/blob/master/notebooks/2-version-control.ipynb)\n",
    "\n",
    "- **Use the Slack channels (<https://bioinfo-course-2020.slack.com>)!**\n"
   ]
  }
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