notebooks/Notebook05-0.ipynb

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   "source": [
    "# Setting up Anaconda"
   ]
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   "source": [
    "Anaconda is a software/environment manager, a very wonderful tool for managing software installations.\n",
    "\n",
    "Launch an instance (I used m4.16xlarge - on-demand, 200 Gb extra EBS). First, get the script from Anaconda Continuum. Go to the [Anaconda distribution](https://www.anaconda.com/distribution/#download-section) download section, click Linux (we're using Linux), then get the link. Then wget the file from the instance."
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  {
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   "source": [
    "![](../images/Notebook05-0/image01.png)"
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   "source": [
    "Next, run the script."
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   "source": [
    "bash Anaconda3-2019.03-Linux-x86_64.sh"
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   "source": [
    "You will be prompted to the license agreement. Read it, click Enter to scroll down, then agree if you agree to the license. Then, specify the location for the Anaconda installation."
   ]
  },
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](../images/Notebook05-0/image02.png)"
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   "source": [
    "Click Enter to continue with the software installation. After the installation finished confirm initialization of Anaconda3."
   ]
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   "source": [
    "![](../images/Notebook05-0/image03.png)"
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   "source": [
    "Now, we can use conda - after sourcing your .bashrc (it was only added just now)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](../images/Notebook05-0/image04.png)"
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   "source": [
    "If you have base in front of the command prompt, then we are on the right track. It means we are in base environment.\n",
    "\n",
    "Supposedly you are working on two bioinformatics projects and one require one software version, the other project with another version, and the two softwares cannot coexist. How?\n",
    "\n",
    "There is where the concept of environment is most effective. Use conda list to list the base environment."
   ]
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](../images/Notebook05-0/image03.png)"
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   "source": [
    "Create a conda environment named env1. While at it, we are going to install cmake on it."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](../images/Notebook05-0/image06.png)"
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   "source": [
    "Try an figure out what each option means.\n",
    "\n",
    "To get into the new environment, use conda activate."
   ]
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](../images/Notebook05-0/image07.png)"
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   "cell_type": "markdown",
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   "source": [
    "List the conda environment. Notice that the list of software is different than when we were on base environment."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](../images/Notebook05-0/image08.png)"
   ]
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Conda deactivate to deactivate env1 environment and to return to base environment."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![](../images/Notebook05-0/image09.png)"
   ]
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