solgenomics/vigs

Stand Alone version of SGN VIGS Tool

VIGS

Stand Alone version of SGN VIGS Tool

Developed on a Catalyst framework

To add a VIGS dataset, use the following commands:

unzip GCA_003287315.1.zip

in emacs, replace the string >lcl| with > , if present (otherwise, fastacmd will not work correctly)

Copy the dataset to the correct location, where the VIGS tool can see it. If using the docker, this target directory has to be mounted into the docker at /home/vigs_sequence_files/.

sudo cp ncbi_dataset/data/GCA_003287315.1/cds_from_genomic.fna /export/prod/blast/databases/current/vigs/Phytophthora_cactorum_GCA_003287315.1_cds.fa

Enter the docker and issue the following command to index the file for BLAST:

docker exec -it vigs_tool bash
cd /home/vigs_sequence_files/

sudo makeblastdb -in Phytophthora_cactorum_GCA_003287315.1_cds.fa -dbtype nucl -out Phytophthora_cactorum_GCA_003287315.1_cds -parse_seqids

Index the file for use with bowtie2:

sudo bowtie-build -f /export/prod/blast/databases/current/vigs/Phytophthora_cactorum_GCA_003287315.1_cds.fa /export/prod/blast/databases/current/vigs/Phytophthora_cactorum_GCA_003287315.1_cds

Installation

A docker build for the VIGS tool is available from docker hub and is the recommended installation method.

Install docker on your system

To install the VIGS tool, first install docker. Refer to the docker installation instructions on the Docker site.

Install git on your system

In Debian, Ubuntu, PoP_OS, etc., install git using apt install git. On other platforms, use the respective packaging systems to install git.

Install the vigs_tool docker

To install the vigs_tool system, clone the git repository that contains the example docker-compose.yml file.

git clone https://github.com/solgenomics/VIGS

Run the vigs_tool from within the VIGS folder using:

docker compose up -d

By default, the VIGS interface will be available at localhost:8088. To make the VIGS tool available through secure http, an nginx front-end is recommended, using an https certificate by Let's encrypt.

To start the server manually

If you install the system manually, you can start the server using the start script in the VIGS/ directory. You can also use this script in the docker.

bash start_vigs.sh

The server needs to be stop by killing the vigs_server.pl process.

vigs's Issues

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