Installing GenEra

Installation

GenEra can be installed using Docker or Singularity. Alternatively, GenEra can also be installed using Conda

Docker and Singularity installation

A Docker image can be pulled using the following command:

docker pull josuebarrera/genera

GenEra can then be used through Docker by running the following command:

docker run --rm -v $(pwd):/working-dir -w /working-dir josuebarrera/genera genEra -q [query_sequences.fasta] -t [query_taxid] -b [path/to/nr] -d [path/to/taxdump]

Alternatively, the image can be converted to .sif format to run GenEra with Singularity:

singularity exec /path/to/genera_latest.sif genEra -q [query_sequences.fasta] -t [query_taxid] -b [path/to/nr] -d [path/to/taxdump]

Conda and mamba installation

GenEra can be installed with conda using the following commands:

conda create -n genera
conda activate genera
conda install bioconda::genera

Alternatively, the user can install GenEra using mamba or micromamba:

mamba create -n genera
mamba activate genera
mamba install -c conda-forge -c bioconda genera

Note

Double-check that the latest version of diamond is installed. If not, run conda update -c bioconda -c conda-forge diamond

Once you finished, you can test whether genEra was installed correctly by running:

wget https://github.com/josuebarrera/GenEra/raw/refs/heads/main/test_files.zip
unzip test_files.zip
bash test_installation.sh -i test_files

If all the tests appear as PASSED, then you are ready to use the software!