> For the complete documentation index, see [llms.txt](https://usdrcg.gitbook.io/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://usdrcg.gitbook.io/docs/non-lawrence-guides/anaconda-installation.md).

# Software Installations on Windows

This page contains instructions for installing Anaconda/Bioconda on Windows, Ubuntu on Windows, Mac, a Lawrence account, and Jetstream

{% hint style="danger" %}
Warning: this site is under construction. The information may be incomplete.
{% endhint %}

## Anaconda on Windows

To download Anaconda, go to the distribution website: <https://www.anaconda.com/distribution/>.

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-0b10230faa97672d538411fb4fc994db268f368d%2FScreenshot%20\(16\).png?alt=media)

Scroll down to the download section. Select "Windows", then select "Download".

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-d071ead61d41a7ec45a3b118c7e17e193865c57f%2FScreenshot%20\(19\).png?alt=media)

Follow the installation wizard.

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-b57434e8f7b77e4d5d3624031c9af711456a7a36%2FAnacondaInstallationSteps.png?alt=media)

The Users Guide should pop up ([this](http://docs.anaconda.com/anaconda/user-guide/getting-started/#open-nav-win) webpage).

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-4dfd5391768c1b8a35067ad7c9e32f8f8c0c9e05%2FScreenshot%20\(34\).png?alt=media)

To open Anaconda, go to the start menu and expand the Anaconda3 folder.

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-3aef2872ab15020b83f761cdf429d5c6fb274d49%2FScreenshot%20\(35\).png?alt=media)

Select "Anaconda Navigator".

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-9498eb502f2490a376bd81cc2efd4a8eb72483fa%2FScreenshot%20\(36\).png?alt=media)

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-1720646eb6f2252694ccbc1eaa3d102e29227515%2FScreenshot%20\(37\).png?alt=media)

## Anaconda on Ubuntu on Windows

### Installing Ubuntu on Windows

Ubuntu for Windows can be downloaded from the Microsoft store.

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-a1c251839297e26bcf9dc577d9bb761cb7882a04%2Fubuntu-1%20\(4\)%20\(4\)%20\(4\)%20\(4\).png?alt=media)

Search for "ubuntu".

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-664ee6f731957121dac350a590da9183a75342dd%2Fubuntu1.png?alt=media)

Select the app.

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-2d62cac8d682539f2d3a1743363d0ebeef414325%2Fubuntu2%20\(1\)%20\(1\)%20\(1\)%20\(1\).png?alt=media)

Click "**Get**", then "**Install**".

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-befba0b125dda1ddabf36d9a9fbaa2199a387bca%2Fubuntu3%20\(2\)%20\(2\)%20\(2\)%20\(2\).png?alt=media)

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-4c7514ae1c4dfbdcefecb91ca435474e5b3f8c89%2Fubuntu4.png?alt=media)

Search for "Ubuntu" and select the app.

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-cb3dd69bf2f62a0f41fe4bdf71e908b4ac9062ee%2FScreenshot%20\(264\).png?alt=media)

The window will look like this:

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-84baa4d84b4118e8414663bb3c6aa89f1fecd16e%2FScreenshot%20\(265\).png?alt=media)

### Installing Anaconda on Ubuntu on Windows

First, open Ubuntu for Windows (see above) and check to ensure that conda is not already installed.

```
user@NI0000:~$ which conda
```

If it has been, a file path will show up under the command, if not, the next line will be a prompt.

![](https://57295520-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LMxcW8l8a9ogs7-hqgF%2Fuploads%2Fgit-blob-92ea2cf3723efa6b4e23bd761dfe3ccc5eae9d8b%2FcondaNotInstalled.png?alt=media)

Download the installer

```
user@NI0000:~$ wget --quiet --no-check-certificate https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64
.sh
user@NI0000:~$ ls
Miniconda3-latest-Linux-x86_64.sh

```

Run the installer

```
user@NI0000:~$ bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/anaconda3
```

```
PREFIX=/home/adison/anaconda3
Unpacking payload ...
…
  zstd               pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0
…
Preparing transaction: done
Executing transaction: done
installation finished.
…

user@NI0000:~$
```

Run an update:

```
user@NI0000:~$ $HOME/anaconda3/bin/conda update conda -y
```

```
Collecting package metadata (current_repodata.json): done
Solving environment: done
 ...

Executing transaction: done
user@NI0000:~$
```

Then install Anaconda

```
user@NI0000:~$ $HOME/anaconda3/bin/conda install anaconda -y
```

```
Collecting package metadata (current_repodata.json): done
Solving environment: done
 
## Package Plan ##
...
Verifying transaction: done
Executing transaction: / b'Enabling notebook extension jupyter-js-widgets/extension...\n      - Validating: \x1b[32mOK\x1b[0m\n'                                                                                                              done
user@NI0000:~$
```

Initialize

```
user@NI0000:~$ $HOME/anaconda3/bin/conda init
```

```
no change     /home/user/anaconda3/condabin/conda
...
no change     /home/user/anaconda3/etc/profile.d/conda.csh
modified      /home/user/.bashrc
 
==> For changes to take effect, close and re-open your current shell. <==
 
user@NI0000:~$
```

Close and re-open your Ubuntu command line.

## Bioconda on Windows on Ubuntu

After running the installation of Anaconda on Ubuntu on Windows (see above), add bioconda:

```
user@NI0000:~$ conda config --add channels bioconda
```