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Login to Cluster + mOTUSv2 Installation (60min)

Login to Cluster + mOTUSv2 Installation (60min)#

The mOTUsv2 tool uses a set of 10 marker genes to profile metagenomic and metatranscriptomic sequencing datasets.

mOTUSv2 is capable of running on different operating systems, uses relatively low memory and can be executed on machines with only a few CPUs. However, in order to process all mOTUSv2 jobs in parallel, we will fall back to use a dedicated compute cluster for today’s tutorial.

We will first log in to the cluster and install the mOTUSv2 tool.

Connection to the cluster (10min)#

Euler is the ETH supercomputer with a large number of compute nodes. During the course you will use Euler to run mOTUsv2. To login to euler you open mobaXterm, start a new session and type:

ssh euler

You will be asked if you trust this connection (type yes) and will then be asked for the password (same as for the VM).

Proceed to your work directory (replace biolcourse-XX with your our username):

cd /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/biolcourse-XX/

This is the same folder as you see it on your Windows Desktop and will serve as data folder for all your computations.

ALL FOLLOWING COMMANDS HAVE TO BE EXECUTED ON EULER AND NOT ON WINDOWS

Quick Linux Introduction (15min)#

Being able to use the Linux terminal is an integral part of most bioinformatic workflows. In order to use mOTUSv2 on Linux we have to know some basic commands:

# print current directory
pwd
# e.g. /cluster/home/biolcourse-XX/

# change to new directory
cd /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/biolcourse-XX/
pwd
# now you are in /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/biolcourse-XX/

# list all files and folders inside the current directory
ls

# list all files and folders inside a specific directory
ls /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/data/

# go one directory up
cd ..
# now you are in /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/

# inspect a file
less /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/data/M01.2-V1-stool-metaG/M01.2-V1-stool-metaG.merged.motus
# Use the cursor to navigate, use space to go one page down, use q to leave the program

Mastering the terminal is an incredible useful skill for most bioinformatic workflows. We show you only the minimum number commands that are needed for this tutorial. There’re great tutorials if you would like to continue working with the terminal.

mOTUSv2 Installation (30min)#

Type pwd and make sure that you are in your working directory (/nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/biolcourse-XX/).

# print current directory
pwd
# /cluster/home/biolcourse-XX/
cd /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/biolcourse-XX/
pwd
# /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/biolcourse-XX/

We will follow the installation instructions from the mOTUSv2 website. At home you can reuse the installation instructions and tutorials from this website.

The mOTUSv2 software is written in python3 and requires the bwa aligner and samtools as prerequisites. All prerequisites are already installed on euler but need to be loaded:

# load bwa, samtools and python
module load vcp
module load samtools
module load python/3.6.0

Next we install the mOTUSv2 software:

# Running the setup.py command will take ~1 minute
wget https://github.com/motu-tool/mOTUs_v2/archive/2.1.1.tar.gz
tar -xzvf 2.1.1.tar.gz
cd mOTUs_v2-2.1.1
python setup.py
export PATH=`pwd`:$PATH
python test.py
cd ..

mOTUSv2 is correctly installed if the last line reads like:

Check resulting profile: correct.

Environment#

You will need to run the following command after each login to the server:

source /nfs/nas22.ethz.ch/fs2201/biol_isg_course_1/Workshop_Bern/bin/configure.sh

Installation at Home#

Installation of mOTUsv2 is very simple. You can either use the package that we provide at bioconda or perform a manual installation similar to the one described above. We recommend to use bioconda as you don’t need to install dependencies by hand. A thorough description on how install mOTUsv2 on any macOS or linux device can be found her: https://motu-tool.org

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