Installation

Installing with conda

EUKulele may also be downloaded as a conda package, which will eventually become the easiest option, as conda automatically installs all dependencies for the user. The package can currently be downloaded via:

conda install -c bioconda -c conda-forge EUKulele

To ensure you have the most recent version of EUKulele, you can run conda update EUKulele, or you can check the EUKulele landing page on Anaconda Cloud to check the most recent version number.

If you find that the conda install is running slowly, you may also, alternatively, follow the steps below to install with mamba.

Installing with mamba

EUKulele can be installed more rapidly remotely using mamba, a parallelized fast installer that is obtainable via conda. In order to install via mamba, the following steps are necessary.

  • Create a conda environment

  • Install mamba, using:

    conda install mamba -c conda-forge

  • Install the package as before, but using mamba as the installer, rather than conda:

    mamba install -c akrinos -c bioconda -c conda-forge EUKulele

This should provide a considerable speedup as compared to conda.

Installing with Pip

There are few different ways to install EUKulele, but the easiest is:

pip install EUKulele

There may some Python dependencies that are not immediately downloaded when EUKulele is pip-installed. If this is the case, the offending dependencies may be installed individually.

The external dependencies can be installed individual, or with conda using:

conda create -n EUKulele
conda activate EUKulele
conda install -c bioconda -c conda-forge blast busco=4.0.6 diamond transdecoder

As the dependencies external to PyPI are:

  • BLAST
  • BUSCO
  • Diamond
  • TransDecoder (if using metatranscriptome samples and the --use_transdecoder flag)

Cloning the Development Code from GitHub

In addition, you can clone EUKulele from GitHub (the current development version) using:

git clone https://github.com/AlexanderLabWHOI/EUKulele

And then invoke EUKulele either by executing the script bin/EUKulele directly, or by installing EUKulele as a local package, by calling the following from the EUKulele directory:

python3 -m pip install -e . --user
python setup.py install  --user

Again, in this case, external dependencies may be installed via:

conda create -n EUKulele
conda activate EUKulele
conda install -c bioconda -c conda-forge blast busco=4.0.6 diamond transdecoder

Or individually for each software.

Invocation

If installed either with pip or conda, EUKulele can be invoked via:

EUKulele <arguments>

Where the minimal command would be:

EUKulele --mets_or_mags <choice of data type> --sample_dir <where samples are located>

In which case EUKulele would be run with mostly parameter defaults and using the MMETSP database, by default.

Less common use cases

EUKulele may also be run as a module within Python. Include the phrase import EUKulele in the header of a Python file. Then, you may execute EUKulele using:

EUKulele.eukulele(config=config_file)

in the case that you have a configuration file to specify (replace the config_file variable with this path), or with:

EUKulele.eukulele(string_arguments=string_of_arguments)

where string_of_arguments is a string containing the non-default EUKulele options you wish to specify.