Install Ubuntu

Steps:

  1. Download and install Ubuntu 22.04.3 LTS (Desktop)
  2. Install Ubuntu, create bioinfoman user. Set new password and keep it private.
  3. After installation finished, create a new user, set bioinfo123 password. 
    sudo adduser fcqb2023
  4. Logout (GUI) session and login using the new user account.

Install and setup miniconda

Steps:

  1. Download and install miniconda in home folder:
mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash

  1. Close and reopen the Terminal (bash)

  2. Disable auto activate base environment

conda config --set auto_activate_base False

  1. Close and reopen the Terminal (bash)

  2. Multi-user conda installation 
    #switch to root/admin user
su bioinfoman
myuser=fcqb2023
mypath=/home/$myuser/miniconda3/condabin/conda
mygroup=bioinformatica-fcqb
#Create a new group
sudo groupadd $mygroup
# Change the group ownership to "mygroup" on the entire directory where Anaconda is installed. Replace /PATH/TO/ANACONDA/INSTALL with the actual path to your installed Anaconda file.
sudo chgrp -R $mygroup $mypath
# Set read and write permission for the owner, root, and the mygroup only. Replace /PATH/TO/ANACONDA/INSTALL with the actual path to your installed Anaconda file.
sudo chmod 770 -R $mypath
# Add users to a group. Replace USERNAME with the username of the user you are adding.
sudo adduser $myuser $mygroup
# switch to normal user (fcqb2023 user) 
exit
  3. Create a new conda environment
conda create --name bioinformatica
  1. install SPADES in the new environment
conda activate bioinformatica
conda install -c bioconda spades
  1. Execute test
spades.py --test
  1. If you got this error: AttributeError: module 'collections' has no attribute 'Hashable', then execute:
sed -i  '126 s/isinstance(key, collections\.Hashable)/isinstance(key, collections\.abc\.Hashable)/' ~/miniconda3/envs/bioinformatica/share/spades-3.13.1-0/share/spades/pyyaml3/constructor.py
  1. Execute test again
spades.py --test

you should get:

========= TEST PASSED CORRECTLY.

THE END!

  1. https://docs.anaconda.com/free/anaconda/install/\
  2. https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html\
  3. https://github.com/ablab/spades/issues/873