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 installation

For a manual conda installation, copy and paste this into your terminal:

git clone https://github.com/josuebarrera/GenEra.git && cd GenEra
chmod +x genEra && chmod +x Erassignment && chmod +x hmmEra && chmod +x tree2ncbitax && chmod +x FASTSTEP3R
git clone https://github.com/caraweisman/abSENSE.git && mv abSENSE/Run_abSENSE.py . && chmod +x Run_abSENSE.py
conda create -n genEra python=3.7
conda activate genEra
conda install -c bioconda -c conda-forge diamond
conda install -c bioconda mcl
pip install -U ncbitax2lin
conda install -c conda-forge -c bioconda mmseqs2
conda install -c conda-forge -c bioconda foldseek
conda install -c anaconda scipy
conda install -c bioconda r-seqinr
conda install -c bioconda r-optparse
conda install -c bioconda r-bio3d
conda install -c r r-tidyverse
conda install -c bioconda r-phytools
conda install -c bioconda orthofinder
CONDABIN=$(which ncbitax2lin | sed 's/ncbitax2lin//g') && mv genEra ${CONDABIN} && mv Erassignment ${CONDABIN} && mv Run_abSENSE.py ${CONDABIN} && mv hmmEra ${CONDABIN} && mv tree2ncbitax ${CONDABIN} && mv FASTSTEP3R ${CONDABIN}

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:

bash test_installation.sh

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