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Installation

Freya Arthen edited this page Feb 20, 2024 · 4 revisions

To install taXaminer, use the python package installer pip. Note: taXaminer is as of yet not published at pypi, thus you need to download this repository and provide pip with the link to the directory for installation.

git clone https://github.com/BIONF/taXaminer.git
pip install ./taXaminer

To install the additional dependencies, use the setup function included in taXaminer. You can install the tools either via conda or locally in a specified directory.

Installation of additional tools

Using conda (installs into the currently active environment):

taxaminer.setup --conda

In a local directory:

taxaminer.setup -o </path/to/tool/directory/>

Setup of database

To download and build the database, use:

taxaminer.setup --db -d </path/to/database/directory/>

Use the following command to use an existing database.

taxaminer.setup -d </path/to/existing_database/directory/>

Dependencies

  • operating system: Unix-based
  • Python >= 3.7
  • Diamond >= 2.1.7