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INSTALL.md

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Installation instructions

While we use Google Colab during the course we got a lot of request to give some pointers on how to get a similar setup as what we used during the course. So here you go 😄

Getting the same setup across different operating systems (Windows, Mac, Linux) and on different architectures (local machine, HPC server, cloud) can be challenging so we will use Miniconda for most steps here and create isolated environments for each part/day of the course. If you already have Miniconda or Anacaonda set up on your own machine, feel free to use that.

Day 1 - Amplicon Sequencing Analysis with QIIME 2

Note that QIIME 2 does not support native Windows, so you will have to use the Windows Subsystems for Linux (WSL) on Windows.

0 - Install Miniconda

You can skip this step if you already have a working conda setup. Otherwise follow the official installation instructions.

After this open a terminal (Mac and Linux) or a WSL terminal on Windows.

1 - Install QIIME 2

We will install QIIME 2 just as described in the official instructions. So please follow the Miniconda intructions here. In short, open a terminal and setup QIIME 2 with the following command where you substitute [OS] with either linux (Linux or WSL) or osx (on Mac)

get https://data.qiime2.org/distro/core/qiime2-2021.8-py38-[OS]-conda.yml
conda env create -n qiime2-2021.8 --file qiime2-2021.8-py38-[OS]-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2021.8-py38-[OS]-conda.yml

2 - Install additonal course requirements

In the last step, download this repository (button on upper right) or use git, change into the course directory and add the additonal requirements.

git clone https://github.com/gibbons-lab/isb_course_2021
cd isb_course_2021
conda env update -n qiime2-2021.8 -f conda_day1.yml
conda activate qiime2-2021.8

This will add the additional packages to the QIIME 2 environment.

3 - Run the notebook

You can now run the course notebook by running.

jupyter lab

and opening 16S.ipynb in the file selecctor on the left. When you run the notebook you should skip the full "Setup" section and jump right to the first QIIME 2 comnmand.

Day 2 - Metabolic Modeling of Bacterial Isolates

0 - Install Miniconda

You can skip this step if you already have a working conda setup. Otherwise follow the official installation instructions.

After this open a terminal (Mac and Linux) and a WSL terminal or Conda Console on Windows.

1 - Replicate Course Setup

In the last step, download this repository (button on upper right) or use git, change into the course directory and add the additonal requirements.

git clone https://github.com/gibbons-lab/isb_course_2021
cd isb_course_2021
conda create -n metabolic_modeling -f conda_day2.yml
conda activate metabolic_modeling

2 - Run the notebook

You can now run the course notebook by running.

jupyter lab

and opening models.ipynb in the file selecctor on the left. When you run the notebook you may skip the full "Setup" section and jump right to downloading your assembly.

3 - Get a real carveME install

You may want to replace the fake carveME from the course with the real deal to run it on your own data. For this run the commands from this section after the previous steps to substitute the fake carveME with the real one.

To run carveME you will need a CPLEX license which you can obtain by signing up for the IBM Academic Initiative. After you get your login activated go to the software section or search and look for "CPLEX" and download the CPLEX Optimizatin Studio for your platform. When you unzip it or urn the installer it will extract the software in a directory that you choose. You will need to remeber the directory where you extract CPLEX to for the next steps.

In the terminal you opened before change into the directory where you extracted CPLEX.

cd /path/to/extracted/files
conda activate metabolic_modeling

You know it's the right folder when you type ls and press enter and it shows you several folder one that is called cplex. Now run the following to setup cplex and install carveME.

Mac

pip install cplex/python/3.8/x86-64_osx
pip install carveme

Linux

pip install cplex/python/3.8/x86-64_linux
pip install carveme

Windows

pip install cplex/python/3.8/x86-64_win
pip install carveme