pegi3s/two-way-blast

A Compi pipeline for finding orthologs using a two-way BLAST approach.

two-way-blast

two-way-blast is a compi pipeline to finding orthologs using a two-way BLAST approach. A Docker image is available for this pipeline in this Docker Hub repository.

two-way-blast repositories

• GitHub
• DockerHub
• CompiHub

Using the two-way-blast pipeline in Linux

In order to use the two-way-blast pipeline, you should run and adapt the following command:

docker run --rm -v /path/to/input/data/dir:/input -v /path/to/output/data/dir:/output pegi3s/two-way-blast -q -- --reference_file <reference_nucleotide> --blast_type <blast_type>

In these command, you should replace:

• /path/to/input/data/dir to the actual path that contains your input FASTA files.
• /path/to/output/data/dir to the actual path where the output files will be created.
• <reference_nucleotide> to the actual name of your reference nucleotide file.
• <blast_type> to the name of the type of BLAST you want to use (either blastn or tblastx).

By default, this command launches the compi pipeline with the default number of parallel tasks (6). In order to launch the pipeline with more parallel tasks, add the --num-tasks <num_tasks> parameter right before the --.

Also note that the -q parameter disables Compi progress logs into the console. Remove it in case you want to see them. In addition, you can also use -o parameter to see log messages of the underlying operations (i.e. BLAST commands).

Test data

The sample data is available here. Download, uncompress it and move to the test-data-two-way-blast directory, where you will find:

• A directory called data, that contains the sample FASTA files.
• A file called run.sh, that contains the following commands (where you should adapt the paths) to test the pipeline:

INPUT_DIR=/path/to/test-data-two-way-blast/data/
OUTPUT_DIR=/path/to/output/data/dir
REFERENCE=nucleotide.fasta
BLAST_TYPE=tblastx
COMPI_NUM_TASKS=8

docker run --rm -v ${INPUT_DIR}:/input -v ${OUTPUT_DIR}:/output pegi3s/two-way-blast --num-tasks ${COMPI_NUM_TASKS} -q -- --reference_file ${REFERENCE} --blast_type ${BLAST_TYPE}

Building the Docker image

To build the Docker image, compi-dk is required. Once you have it installed, simply run compi-dk build from the project directory to build the Docker image. The image will be created with the name specified in the compi.project file (i.e. pegi3s/two-way-blast:latest). This file also specifies the version of compi that goes into the Docker image.