tripal_blast: A PHP repository from dsenalik

INTRODUCTION

This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+.

Specifically it provides blast program-specific forms (blastn, blastp, tblastn, blastx are supported). In the future, there will be a single form where you will be able to select either a nucleotide or a protein database to BLAST against regardless of the type of query and it will decide which BLAST program to use based on the combination of query/database type (ie: if you selected a protein database on the nucleotide BLAST form then blastx would be used).

BLAST submissions result in the creation of Tripal jobs which then need to run from the command-line. This ensures that long running BLASTs will not cause page time-outs but does add some management overhead and might result in longer waits for users depending on how often you have cron set to run Tripal jobs. You can alternatively use the Tripal Jobs Daemon to automate running of Tripal Jobs reducing user wait time and your own workload.

The BLAST results page is an expandable summary table with each hit being listed as a row in the table with query/hit/e-value information. The row can then be expanded to include additional information including the alignment. Download formats are allow users to download these results in the familiar tabular, GFF3 or HTML NCBI formats.

Installation

Install NCBI BLAST+ on your server (Tested with 2.2.26+). Please use the official NCBI installation documentation for your server.
Install this module as you would any Drupal module (ie: download, unpack in sites/all/modules and enable through http://[your site]/admin/modules)
Create "Blast Database" nodes for each dataset you want to make available for your users to BLAST against. BLAST databases should first be created using the command-line makeblastdb program with the -parse_seqids flag.

It's recommended that you also install the Tripal Job Daemon to manage BLAST jobs and ensure they are run soon after being submitted by the user. Without this additional module, administrators will have to execute the Tripal jobs either manually or through use of cron jobs.

Documentation

We have an extensive user guide and a developer guide available via readthedocs.

Comparison with other Modules

	Tripal BLAST UI	Tripal BLAST Analysis
Provides an interface to execute BLASTs	Yes	No
Display BLAST Results to users	After BLAST submission	On associated feature pages
Load BLAST Results into Chado	No	Yes

NOTE: These modules will be combined into a single download available here in Tripal 4.

Future Development

Improvements to XML reader for support of larger result sets
The ability to blast against 2+ datasets at the same time
Ability to Email user when BLAST is done
Automatic cleaning up of BLAST job files after 1 week (make time frame configurable)

Testing or Development via Docker

Testing or development of this module can be done through laceysanderson's Drupal 7, Tripal 3 docker image using the following instructions.

Pull the most recent image from the Github Package Repository.

docker pull laceysanderson/drupal7dev

Pull the Tripal BLAST module. I suggest creating a dockers directory to ensure you can find the directory mapped to your container ;-p

cd ~/Dockers
git clone https://github.com/tripal/tripal_blast
cd tripal_blast

Create the needed .env file. This will not be committed to the repository since it's included in the .gitignore file and could provide security issues.

touch .env

Now edit this file with your favourite editor to include the following variables. Make sure to change the values for security reasons!

##
## DO NOT REMOVE ANY VARIABLES.
##
DBADMIN=tripaladmin
DBNAME=tripaldb
DRUPALADMIN=tripaladmin
DRUPALEMAIL=tripaladmin@yourserver.com
SITENAME="Tripal BLAST Docker"

Create a running container exposing the website at localhost:8888 and mounting your current directory inside the container.

Make sure to change DBPASS and ADMINPASS for security reasons.
Your website admin is the value of DRUPALADMIN in the .env file with the password set in the run command below.

docker run --publish=8888:80 --name=tblast -tid \
  -e DBPASS='somesecurepassword' \
  -e ADMINPASS='anothersecurepassword' \
  --env-file=.env \
  --volume=`pwd`:/var/www/html/sites/all/modules/tripal_blast \
  laceysanderson/drupal7dev:latest

Provision the container including installation of the software stack including default configuration. This step will take a few minutes.

docker exec -it tblast /app/init_scripts/startup_container.sh

NOTE: You will need to install NCBI Blast+ and this module on the docker container as we have not yet automated this process.

Now any changes you make in your current directory will be mirrored within the tblast docker container. You can interact with the Tripal site at localhost:8888 in your browser.