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Installation

Operating system

There is no restriction as far as we are aware of. Tested and working on Linux, macOS and Windows systems.

Software environment

Woltka is written in Python 3. One needs at least Python 3.6 to run the program.

We recommend Conda for managing Python version and packages. One can create a conda environment for Woltka by:

conda create -n woltka python=3
conda activate woltka

If you already have a QIIME 2 environment, these steps can be omitted as the dependencies are already included. See details.

You may also use Mamba instead of Conda. The procedures discussed in this page that apply to Conda also apply to Mamba.

Installation

Option 1: Install the latest release from the Bioconda channel:

conda install -c conda-forge -c bioconda woltka
  • Note: It is necessary to also specify the conda-forge channel, in order to install the latest version of biom-format, a dependency of Woltka.

Option 2: Install the latest release using pip:

pip install woltka

Option 3: Install the current development from GitHub:

pip install git+https://github.com/qiyunzhu/woltka.git

Option 4: Install from a local copy:

Download this repository or any of the previous releases. Unzip and navigate to the package directory. Then execute:

python setup.py install

Type woltka to check if installation is successful, in which case command-line help information will be displayed on the screen.

Acceleration

Woltka has a Numba-accelerated version (the numba branch) in parallel to the master branch. In this version, the "coord-match" algorithm for functional analysis (see details) is significantly faster and consumes less memory. To use this feature, install Woltka using the following commands instead:

conda install -c conda-forge numba biom-format
pip install git+https://github.com/qiyunzhu/woltka.git@numba

[Note] This feature only accelerates read-gene matching. It does not help with the analysis of microbiome structure.

Upgrade

If you installed Woltka using Conda, do:

conda update -c conda-forge -c bioconda woltka

If you installed Woltka using pip, do:

pip install -U woltka

Uninstallation

If you installed Woltka using Conda, do:

conda remove woltka

If you installed Woltka using pip, do:

pip uninstall woltka

If you no longer need the Conda environment:

conda env remove -n woltka

Compatibility

If in the future some dependencies have changes that are not compatible with the current release of Woltka, the following "safe" commands can be used to install the current versions of dependencies.

conda create -n woltka python=3.10.8
conda activate woltka
conda install -c conda-forge biom-format=2.1.13
conda install -c bioconda woltka=0.1.5

Test

You may test whether Woltka functions correctly by running it on some small test datasets. You will need to download the repository to get them. See example usage for how to run these small tests manually. Alternatively, you may execute the following command in the repository directory:

python -m unittest

This will run all tests automatically. If it prints "OK" in the end, everything is okay. Otherwise it will report specific error(s), and in such case, please contact the development team for solutions.