Software Installations on Windows

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

Warning: this site is under construction. The information may be incomplete.

Anaconda on Windows

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

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

Follow the installation wizard.

The Users Guide should pop up (this webpage).

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

Select "Anaconda Navigator".

Anaconda on Ubuntu on Windows

Installing Ubuntu on Windows

Ubuntu for Windows can be downloaded from the Microsoft store.

Search for "ubuntu".

Select the app.

Click "Get", then "Install".

Search for "Ubuntu" and select the app.

The window will look like this:

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.

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