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Format

Open Anaconda using either of the following 2 methods: Searching it on the Cortana search bar located on the bottom left of screen and choose 'Anaconda Navigator' Click windows start menu on the bottom right. Find the 'Anaconda3 (64-bit)' folder. A drop down menu will appear. Click Anaconda Navigator. Anaconda Navigator is a desktop GUI that comes with Anaconda Individual Edition. It makes it easy to launch applications and manage packages and environments without using command-line commands. Expedite your data science journey with easy access to training materials, documentation, and community resources including Anaconda.org. I deleted the Anaconda- Navigator but it's still on the dock of my Mac. When I right-click on it it says not responding and I can't even force quit it. The app isn't anywhere else just on my dock.

The workshop consists of explanatory discussions interspersed with hands-on exercises. We strongly encourage you to bring a laptop with all required packages installed in order to fully participate. We will also have office hours with CZI computational biology staff available in the morning to help troubleshoot any installation issues before class begins.

Installation guide (before class)

1. Install Python via Anaconda

Even if you have previously installed Python, please install Anaconda for Python version 3 (available on OSX, Linux, and Windows). You can simply click through the install wizard (no customization required, all the defaults are fine).

Anaconda is package manager, which means that it helps coordinate your Python installation and related packages (useful code written by other people for performing specific tasks) for you so that you have a consistent environment (the version of Python and the version of the code in each package that your computer looks at when doing your analysis).

You should now see an icon for 'Anaconda Navigator' in your Applications folder (mac) or the Start menu (Windows). Please contact the instructors if you do not see this icon!

2. Install required packages (for Mac OS)

2A. Install Bioconda

Not everyone who uses Anaconda is a biologist. As a result, some biology-specific packages are only available in the Bioconda channel (collection of packages).

  • Open Anaconda Navigator.
  • Click on Environments in the left sidebar
  • Click on Channels in the top middle of the screen
  • Click on Add...
  • In the bottom text box, type bioconda and press Enter
  • Press Update channels
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2B. Download the course config file

To handle installation of all the Python packages required for the workshop (both days, all tracks), we have prepared a configuration file that tells Anaconda how to configure your environment.

  • Download the configuration file called sfn-workshop-mac.yml here. Save it an a spot you'll remember.
  • Open Anaconda Navigator
  • Click on Environments in the left sidebar
  • Click on Import in the bottom left
  • Enter sfn-workshop as the Name, and browse for the sfn-workshop-mac.yaml file you just downloaded
  • Press Import

2. Install required packages (for windows)

2A. Download the course config file

To handle installation of all the Python packages required for the workshop (both days, all tracks), we have prepared a configuration file that tells Anaconda how to configure your environment.

  • Download the configuration file called sfn-workshop-windows.yml here. Save it an a spot you'll remember.
  • Open Anaconda Navigator
  • Click on Environments in the left sidebar
  • Click on Import in the bottom left
  • Enter sfn-workshop as the Name, and browse for the sfn-workshop-windows.yaml file you just downloaded
  • Press Import

2B. Install scanpy (for Windows users in the single-cell track only)

  • Click on the green play button next to the sfn-workshop and choose 'Open terminal'
  • Enter python3 -m pip install scanpy and press Enter

3. Check your installation

  1. Open Anaconda Navigator
  2. Click on Environments in the left sidebar
  3. Select the sfn-workshop environment from the list. This may take several minutes.
  4. Click on the green play button that appears
  5. Select Open with Jupyter Notebook from the list

You should get a browser tab that says 'Jupyter' at the top and lists all the files on your computer. This might not seem like much, but is all you need to get started! :)

If this does not work, please come to office hours before class so the CZI computational biology team can help you

4. Download course files

For the imaging track

Go to https://github.com/sofroniewn/2019-ndcn-comp-bio-imaging

For the single cell track

Go to https://github.com/chanzuckerberg/scRNA-python-workshop

Clone or download contents

If you are comfortable cloning a repository with git, we encourage you to do so. Otherwise, click the green 'clone or download' button and choose 'download zip'. We encourage you to do this the evening before class, as we may make some last-minute updates to the material.

5. Bonus: install fun visualization tools (optional)

  1. Open a terminal window (Mac: Applications > Utilities > Terminal; Windows: Start > Windows System > Command Prompt)

For the imaging track:

  1. In the terminal window, copy and paste the following and press Enter:

    python3 -m pip install napari

To test your installation of napari, type napari in the next terminal line and press Enter. You should see an application window open up.

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For the single-cell analysis track:

  1. In the terminal window, copy and paste the following and press Enter:

    python3 -m pip install cellxgene

To test your installation of cellxgene, type cellxgene in the next terminal line and press Enter. You should see something like this:
Usage: cellxgene [OPTIONS] COMMAND [ARGS]... Options: --version Show the version and exit. --help Show this message and exit. Commands: launch Launch the cellxgene data viewer. prepare Preprocesses data for use with cellxgene.

If this does not work, and you would like to try out the visualization tools in class, please come to office hours before class so we can help you.

System requirements¶

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Operating systems: Navigator supports the same operating systems thatthe Anaconda Distribution supports. These include:

  • Windows 8 or newer, 32-bit or 64-bit.
  • macOS 10.13+, 64-bit.
  • Ubuntu 14+/Centos6+, 64-bit.

Python: Versions 2.7, 3.6, 3.7, and 3.8.

To use Navigator in online mode, you must be able to reach these sites, so you may need to add them to a whitelist in your network’s firewall settings.

  • https://repo.anaconda.com for repositories and installers
  • https://conda.anaconda.org for conda-forge and other channels on Anaconda Cloud (anaconda.org)
  • google-public-dns-a.google.com (8.8.8.8:53) to check internet connectivity with Google Public DNS

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Installing Navigator¶

Navigator is automatically installed when you install Anacondaversion 4.0.0 or higher.

If you have Minicondaor an older version of Anaconda installed, you can install Navigator from an Anaconda Promptby running the command condainstallanaconda-navigator.

To start Navigator, see Getting Started.

Uninstalling Navigator¶

To uninstall Anaconda Navigator, open the Anaconda Prompt (terminal on macOS orLinux), and enter this command:

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To uninstall all of Anaconda see Uninstalling Anaconda.

Configuring Navigator to work with a local Anaconda Repository¶

If you’re an Anaconda Enterprise subscriber, you can configureNavigator to search for packages in your local Anaconda Repositoryinstead of searching on Anaconda.org.

To configure Navigator to search in a local Anaconda Repository:

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  1. In the top menu bar’s Anaconda Navigator menu (on macOS it’s File),select Preferences.

  2. In the Anaconda API domain field, type the address of your localAnaconda Repository.

  3. Click the Apply button.

  4. At the top of the Navigator window, click the Sign in to Anaconda Cloud button.

  5. In the Username and Password fields, type your Anaconda Repositoryusername and password.

  6. Click the Login button.