NCBI IgBLAST command line application in a Docker image.
IgBLAST image can be run following standard docker methods. Some examples are shown below (assuming your image version is 1.21.0 and work directory has a folder named "database" that has the germline gene databases you want to search and a folder named "query" that has your query sequence file).
- To run interactively, issue the command:
docker run -e IGDATA=/ncbi-igblast-1.21.0 -v $HOME/database:/d -v $HOME/query:/q -it ncbi/igblast
You will get a docker terminal like this:
root@27af8892c20b:/#
To run igblastn, simply issue:
igblastn -query /q/temp.query -germline_db_V /d/human_gl_V -germline_db_D /d/human_gl_D -germline_db_J /d/human_gl_J -show_translation -auxiliary_data optional_file/human_gl.aux -organism human
- You can also run the image directly as follows:
docker run -e IGDATA=/ncbi-igblast-1.21.0 -v $HOME/database:/d -v $HOME/query:/q ncbi/igblast igblastn -query /q/temp.query -germline_db_V /d/human_gl_V -germline_db_D /d/human_gl_D -germline_db_J /d/human_gl_J -show_translation -auxiliary_data optional_file/human_gl.aux -organism human
Note that this image contains only IgBLAST executable for Linux platform. The IgBLAST documentation is at https://ncbi.github.io/igblast/
A Makefile is provided to conveniently maintain this docker image. In the commands below, the value of $X represents the version of NCBI IgBLAST to base this image on.
make build VERSION=$X: builds the docker imagemake publish VERSION=$X: publishes the image to Docker Hubmake check: performs a sanity check on the most recently built image