This page is the memo about installing miniconda (conda command) on Fedora Linux. I referred the document [1]. I wanted to install a bioconda package. Because I wanted to build a Galaxy tool using Planemo [2]. The tutorial is using bioconda. I am also trying to create my first bioconda package seeing this document [3].
The conda is command. bioconda is a repository. As a note, I was told that conda has open source license.
Anyway, when installing conda, we need to decide we install miniconda or anaconda. Seeing this document [4], Anaconda is conda command + some conda packages. So, I selected miniconda as a small start.
Download the installer.
$ wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh $ sha256sum Miniconda3-py39_4.10.3-Linux-x86_64.sh 1ea2f885b4dbc3098662845560bc64271eb17085387a70c2ba3f29fff6f8d52f Miniconda3-py39_4.10.3-Linux-x86_64.sh
Execute the installer.
$ bash Miniconda3-py39_4.10.3-Linux-x86_64.sh Welcome to Miniconda3 py39_4.10.3 In order to continue the installation process, please review the license agreement. Please, press ENTER to continue ... Do you accept the license terms? [yes|no] [no] >>> yes Miniconda3 will now be installed into this location: /home/jaruga/miniconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/home/jaruga/miniconda3] >>> [Enter] ... installation finished. Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] [no] >>> yes no change /home/jaruga/miniconda3/condabin/conda no change /home/jaruga/miniconda3/bin/conda no change /home/jaruga/miniconda3/bin/conda-env no change /home/jaruga/miniconda3/bin/activate no change /home/jaruga/miniconda3/bin/deactivate no change /home/jaruga/miniconda3/etc/profile.d/conda.sh no change /home/jaruga/miniconda3/etc/fish/conf.d/conda.fish no change /home/jaruga/miniconda3/shell/condabin/Conda.psm1 no change /home/jaruga/miniconda3/shell/condabin/conda-hook.ps1 no change /home/jaruga/miniconda3/lib/python3.9/site-packages/xontrib/conda.xsh no change /home/jaruga/miniconda3/etc/profile.d/conda.csh modified /home/jaruga/.bashrc ==> For changes to take effect, close and re-open your current shell. <== If you'd prefer that conda's base environment not be activated on startup,- set the auto_activate_base parameter to false:- conda config --set auto_activate_base false Thank you for installing Miniconda3!
Now the .bashrc was modified adding the following code at the end of the file. I want to move this logic to another file, calling it as source foo.sh.
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/jaruga/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/home/jaruga/miniconda3/etc/profile.d/conda.sh" ]; then
. "/home/jaruga/miniconda3/etc/profile.d/conda.sh"
else
export PATH="/home/jaruga/miniconda3/bin:$PATH"
fi--
fi
unset __conda_setup
# <<< conda initialize <<<
I wanted to avoid calling conda initially. So, I executed the following command.
$ conda config --set auto_activate_base false
Here are the commands to activate and deactivate the conda mode. It's like virtualenv.
$ conda activate (base) $ conda deactivate $
