NRP DTP CSB1 Practical on Qiime2

To try the Qiime 2 tutorial you'll need a Linux machine, you can either:

  • Use a Virtual Machine, and then skip to “Install Miniconda”
  • Use a terminal emulator to connect to the training server, as described below

:!: IMPORTANT: If you fail logging in more than two times, you'll block the access for all the users, yourself included, for 15 minutes.

  • Server: learning.seq.space
  • Username (DTUxx) and Password as provided

If you never logged in into a Linux server, please check this manual first:

Miniconda is a very popular package manager for Linux. Think of Miniconda as an App Store: it's a program that will easily install any bioinformatic program for us, in our “user space”. It's so good, that it's worth trying to see how to install it:

Download the installer first. wget is a command line tool to download a file from a website (URL):

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

Run the installer that you just downloaded with the following command:

bash "Miniconda3-latest-Linux-x86_64.sh" -b -p $HOME/miniconda3

Now it's time to configure our “App Store”. Add conda to the startup list:

echo ". $HOME/miniconda3/etc/profile.d/conda.sh" >> $HOME/.bashrc
source $HOME/.bashrc

Finally, we'll add relevant repositories (i.e. add some shelves to our store):

conda config --add channels r
conda config --add channels conda-forge
conda config --add channels bioconda

Did the installation work? First, let's see if we have conda now, typing the following command:

conda --version

If you get an error like command not found, there's something to fix!

We can now remove the installer:

rm Miniconda3-latest-Linux-x86_64.sh

Using Miniconda we'll create a dedicated environment called qiime2-2019.1 to install Qiime2 and all its dependencies there:

wget "https://data.qiime2.org/distro/core/qiime2-2019.1-py36-linux-conda.yml"
conda env create -n "qiime2-2019.1" --file "qiime2-2019.1-py36-linux-conda.yml"
# OPTIONAL CLEANUP
rm "qiime2-2019.1-py36-linux-conda.yml"

Now you can “activate” qiime2 by:

conda activate qiime2-2019

And then you'll have the tools needed to run the Qiime 2 tutorial