vimalkvn/viga repository overview

⁠Attention

June 11, 2022

This Docker image is no longer up to date. Instead, please use the install script in the developer⁠ branch of EGTortuero/viga.

⁠A Docker image for VIGA

This is a Docker⁠ image for running VIGA⁠ in a container. If you have installed Docker, you can pull this image using:

docker pull vimalkvn/viga

In addition to the VIGA script from the Github repository, this image has all dependencies pre-installed — Aragorn, HMMER, Prodigal, BioPython, LASTZ, Tandem and Inverted repeats finder

⁠Note regarding databases

If you have all the necessary databases downloaded and formatted correctly, you can start using this container immediately. The create_dbs.sh⁠ script included in this repository automates this process of downloading and formatting databases.

The methods below assume these databases (--blastdb, --rfamdb and --hmmerdb) are located in /data/databases. If this is not the case, please modifythe wrapper script or the command accordingly. A simple approach would be to save all databases in one location and export the top level directory using the -v option of the docker command.

⁠Using this Docker image

Once databases are setup, select from one of the following methods to run a container — using the wrapper script or running a container directly.

In both cases, input files are assumed to be present in the directory where the command is run.

Other VIGA program options can be specified and are sent as is.

⁠Option 1. Use the wrapper script (recommended)

Note: This script requires sudo access as it calls the docker command. Administrators can restrict sudo access to just this script in /etc/sudoers if required.

Download the run-viga⁠ wrapper script available from this repository, save it in a location accessible in the PATH, for example, /usr/local/bin, make it executable and then run it like this:

sudo run-viga --input rubella.fasta \
--diamonddb /data/databases/refseq_viral_proteins \
--blastdb /data/databases/refseq_viral_proteins \
--hmmerdb /data/databases/pvogs.hmm \
--rfamdb /data/databases/Rfam.cm \
--modifiers modifiers.txt

⁠Option 2. Run a container directly using docker

Note: The user(s) running this command should be in the docker group.

docker run --rm \
-e LOGNAME=$(logname) \
-e USER=$(logname) \
-u ${UID}:${UID} \
-v /data/databases:/data/databases:ro \
-v $(pwd):/wdir \
-w /wdir \
vimalkvn/viga \
python /program/VIGA.py \
--input rubella.fasta \
--diamonddb /data/databases/refseq_viral_proteins \
--blastdb /data/databases/refseq_viral_proteins \
--hmmerdb /data/databases/pvogs.hmm \
--rfamdb /data/databases/Rfam.cm \
--modifiers modifiers.txt

The -e and -u options are used so that the container has permissions to read input files and the generated output files will be owned by the user running the container and not root.