Busco - weaponsforge/fastractor GitHub Wiki

The following notes describe how to install and run busco from its Docker image.

• CentOS 8
  • With Docker and Docker Compose installed
  • Read on the the Docker installation set-up sections from a Docker demo project for more information.
    • Prerequisites
    • Docker Installation
    • Docker Post Installation
    • Install Docker Compose (Optional) - required for running Busco on Docker

1. Pull the busco Docker image.
   docker pull ezlabgva/busco:v5.beta.1_cv1
2. Create a working directory.

   cd ~/
   mkdir myfolder
   cd myfolder
   

3. Verify the installed busco version. Be sure to cd inside the working directory created on #2, if you haven't already done so.
   docker run -u $(id -u) -v $(pwd):/busco_wd ezlabgva/busco:v5.beta.1_cv1

1. cd into your working directory.
   cd myfolder
2. To use a custom config.ini file to set run parameters:
   • Extract the config.ini that is inside the container to your local working directory.
     docker run -u $(id -u) -v $(pwd):/busco_wd ezlabgva/busco:v5.beta.1_cv1 cat /busco/config/config.ini > myconfig.ini
   • Edit and save the extracted file:
     nano myconfig.ini
   • Run the busco container, using your edited config file. For example:
     docker run -u $(id -u) -v $(pwd):/busco_wd ezlabgva/busco:v5.beta.1_cv1 busco -i genome.fna --config=/busco_wd/myconfig.ini
3. Use the other busco commands to process data. But instead of the shorthand busco <arguments> (when busco is installed using manual installation), use:
   • docker run -u $(id -u) -v $(pwd):/busco_wd ezlabgva/busco:v5.beta.1_cv1 busco <arguments>
     because we're running busco from a Docker container.

   INFO: Always keep in mind to cd into a valid working directory before running the docker busco commands, or busco will fail.