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W1_L01

Intro to the course & software installation

↗ View slidesPractical Notes

software installation instructions

What is needed for the practicals of this course can be subdivided into:

  • packages that can be installed using conda
  • a handfull of GUI executables

conda + packages

Conda is an open source package management system and environment management system for installing multiple versions of software packages and their dependencies and switching easily between them. Look here for a nice cheet-sheet!

To intall conda follow the easy steps described here.

Then what you have to do is just create a new conda environiment and activate it.

conda create --name MP26_env #create the environiment just the first time
conda activate MP26_env # activate the environiment when doing the practicals

Then it is possible to install packages inside it. You can try to google the name of the package + conda, but generally the syntax is conda install channel::package. Here are (most) of the packages you will need!

conda install bioconda::orthofinder
conda install bioconda::mafft
conda install bioconda::trimal
conda install bioconda::AMAS
conda install bioconda::iqtree
conda install bioconda::phylobayes-mpi
conda install bioconda::astral-tree
conda install bioconda::paml

When you want to get outside the environiment use conda deactivate and subsequently to reactivate it conda activate MP26_env.

Special fix for windows!

If you are a Windows PC user I highly recommend installing WSL (Windows Subsystem for Linux). This way, you can work in a Linux environment directly from your Windows PC without the need for a virtual machine. Open the PowerShell and type wsl --install. This command will install WSL with the default Linux distribution (usually Ubuntu). After installation, restart your computer if required and open WSL by runningwsl which will launch your Linux terminal, where you can proceed with setting up Anaconda and other tools.

Special fix for M series macbooks!

When you u create the conda environiment use the flag --platform osx-64 so that the command is: conda create --platform osx-64 --name MP25_env.

After that you might incounter also some problems while running Orthofinder2. If so:

  • Open the parallel_task_manager.py file: nano .../miniconda3/envs/NAME_OF_YOUR_ENVIRONIMENT/bin/scripts_of/parallel_task_manager.py

  • Add the following lines at the very top (before imports):

import multiprocessing
multiprocessing.set_start_method("fork", force=True)

And then any python error should disappear!

Special fix for failed conda installations!

If you can not suceed in installing packages such as phylobayes, you can try to add channels such as conda-forge, and also try to change their order. Something like from this conda install -c conda-forge -c bioconda ph-mpi to this conda install -c bioconda ph-mpi -c conda-forge.

GUI executables

Here are all the GUI software we will use:

  • Aliview - to visualize multiple sequence alignement
  • FigTree - to visualize phylogenies
  • Tracer - to explore statistics of Bayesian Inferences
  • Rstudio and R - to perform some (phylogenetic) data analysis and plotting

Kickstart the practicals

Clone the entire git repo and move into the correct directory.

git clone https://github.com/for-giobbe/MP26
cd ./MP26

All code of the markdown files should be lunched from the main directory, if not specified otherwise.

During the first week of classes, you can get some confidence with the command line if you are not - using this tutorial

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