Bleeding-edge comparative genomics automation and standardization software
Project description
CITING
If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line.
UPDATE
Mycotools is currently in an advanced beta state with frequent updates. It is recommended to run the following in your conda environment if you are having trouble with analyses:
python3 -m pip install mycotools --upgrade
NOTE: Make sure the conda environment is active when updating.
I recommend updating with pip
because the conda
distribution
is currently prone to dependency issues and will not update reliably.
INSTALL
1. Installing miniconda
Miniconda3 is a software environment manager:
curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > ~/miniconda3.sh
bash ~/miniconda3.sh
Activate miniconda and initialize it so it starts up automatically
source activate base # if this fails run conda activate base
conda init
2. Setting up miniconda
Setup and prioritize channels for your miniconda installation. This step must be completed for new and old installs.
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
3. Installing mycotools
Make sure conda
is active, usually by seeing (base)
in in your shell.
If not, try conda activate base
or source activate base
.
conda create -n mycotools mycotools -c xonq -y
conda activate mycotools
python3 -m pip install mycotools --upgrade
mtdb -d
NOTE: There is an unfortunate build dependency conflict with the conda package,
so be sure to explicitly run pip install
as noted above to update the
mycotools package inside the conda environment.
Determine if you are going to link to an already installed database, or become the administrator of a new one:
4a. USER: Integrate with already initialized MycotoolsDB
To link with an existing database, fill in <PATH>
with the database path
mtdb --init <DB_PATH>
You're good to proceed to the usage guide!
4b. ADMINISTRATOR: Initialize a local MycotoolsDB
mtdb update --init <DB_PATH>
A NOTE ON THE CODE
Each standalone script is written with __name__ == '__main__'
, designed to
handle running the script from the command line, as well as main
function(s),
which are importable modules executing the purpose of the script. This enables Mycotools
to be a pipelining-friendly software suite, both from a command line and
python scripting standpoint.
Code edits should focus on stabilizing existing features and simplifying/decerasing the code base. I try to implement code aligned with principles of the functional programming paradigm and modifications should act in accord with this paradigm, i.e. sparing implementation of new classes, limited necessary abstraction, no hidden state changes, and function-based flow.
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