Installing script dependencies

All dependencies can be installed manually, as long as they in your $PATH. However, one of the options below is recommended.

filter_mega353.py

The dependencies for filter_mega353.py are:

• Python (tested with Python version 3.7)
• BioPython (tested with version 1.76)
• pandas.

Installing with conda

If you are using the conda package and environment manager (recommended), you can create a new environment for the NewTarget scripts and install the dependencies as follows:

conda create --name NewTargets python=3.7
conda activate NewTargets
conda install -c anaconda biopython=1.76
conda install pandas

You should then be able to run the script successfully. To exit the conda NewTargets environment, use the command:

conda deactivate

Using a Singularity container

Set this up...

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BYO_transcriptomes.py

This script has some additional dependencies. The full list of requirements is:

• Python 3.7 or higher
• BioPython 1.76 or higher
• EXONERATE 2.4.0
• HMMER 3.2.1 or higher
• MAFFT 7.407 or higher

Installing with conda

You can use the conda NewTargets environment to install the additional dependencies. Enter the environment (conda activate NewTargets) and install as follows:

Make sure you've added the bioconda channel with the commands:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then, install the dependencies with the commands:

conda install -c bioconda exonerate=2.4.0
conda install -c bioconda hmmer
conda install -c bioconda mafft

You should then be able to run the script successfully. To exit the conda NewTargets environment, use the command:

conda deactivate

Using a Singularity container

Set this up...