danny-dirksen/ORFanID

ORFanGenes Instructions

1. How to Run an Example Sequence

1. Visit the ORFanGenes website and click on "Input" from the Navigation bar, or "Get Started" at the bottom of the page.
2. Click on the "Example" link on the bottom left. The text fields will automatically get filled with an example input sequence of genes of E. Coli.
3. The E-Value defaults to e-3 and the Maximum Target Sequences for BLAST defaults to 1000. If these need to be changed, "Advanced Parameters" can be selected and move the slider to select the appropriate values.
4. Select "Submit" and wait for around 10 minutes or more until ORFanGenes processes the input sequence and returns the results.
5. View the results of the example sequence

The example input contains three genes. Out of the three genes, two of which are Genus Restricted Genes, and the other is an ORFan Gene. The Blast Results table shows the taxonomies (and their parents) for each gene in the input sequence from the BLAST search.

2. Using ORFanGenes

1. Visit the ORFanGenes website and click on "Input" from the Navigation bar, or "Get Started" at the bottom of the page.
2. Select the type of sequence (Protein or Nucleotide) that will be processed.
3. Click “Browse” and upload a sequence file. The file must be in .fasta format, and must contain the geneid value of each gene
4. Begin typing the input organism’s name and select the name from the suggested results, and select the organism from the dropdown menu.
5. Select “Advanced parameters” and adjust the maximum E-value and maximum target sequences for BLAST.
6. Click “Submit” and wait for results to load. The time taken for the results to be obtained is dependent on the number of input sequences, selected e-value, and number of target sequences.

4. Deployment

4.1 Prerequisite

Following Software packages needs to be installed in your machine:

1. Docker [sudo apt install maven && sudo apt install docker.io]
2. docker-compose [sudo apt install docker-compose && sudo service docker start && sudo usermod -aG docker ${USER} ]
3. Git
4. Maven [sudo apt install maven]

(Reboot is required after installing all the softwares)

4.2 Deploy the ORFanID

4.2.1 Deploy database api

1. check out git@github.com:orfanid/orfanbasePostgres.git and open it from your IDE(i.e IntelliJ)
2. cp config/application.yml src/main/resources
3. docker-compose up --build -d

4.2.2 Deploy ORFanID App

1. check out git@github.com:orfanid/orfanbasePostgres.git and open it from your IDE(i.e IntelliJ)
2. Change the following values based on your environment if you are using it locally
   • db.api.baseUrl in config > application.yml
   • data.outputdir in config > application.yml
   • app.dir.root in config > application.yml
   • services.blastservice.volumes in docker-compose.yml`
     3 docker-compose up --build -d

4.2.3 Connect both app and api

docker network connect orfanbasepostgres_orfanid orfanid-app
// check if webapp got connected with database api
docker network inspect orfanbasepostgres_orfanid

4.3 Deploy on Cloud/Linux

mkdir -p apps/orfanbase
mkdir -p apps/orfanid

cd apps/orfanbase
git clone git@github.com:orfanid/orfanbasePostgres.git
cd orfanbasePostgres
cp config/application.yml src/main/resources  
docker-compose up --build -d

cd apps/orfanid
git clone git@github.com:orfanid/orfanid.git
cd orfanid     
docker-compose up --build -d

docker network connect orfanbasepostgres_orfanid orfanid-app

// check if webapp got connected with database api
docker network inspect orfanbasepostgres_orfanid

Start server

Run the docker-compose up --build command to build and run the container.

Stop server

If you want to terminate the instance and remove the container, you can use docker-compose down