These are the result files we want to use in the pipeline. "" and "3": Augustus annotation results.We have a special tool for this purpose:ĭetailed information about the Braker2 output can be found at. After the job is finished, you will need to get back the ownership of the output results. When you run a software in Docker, you run it as root. "-rm": remove the docker container after the run finishes." -species=mySpecies -genome=genome.fa.masked -bam= -softmasking -cores=8" is the Braker commands, modify the parameters as needed.( The directory name "/data" within Docker container is hard coded, so do not change) "-v /workdir/$USER/project2:/data" is to mount your data directory "/workdir/$USER/project2" to "/data" in the Docker container.On BioHPC, the data directory must be under "/workdir/$USER", as "docker1" cannot access files outside "/workdir/$USER".1) genome assembly file 2)RNA-seq bam file 3) Genemark directory "gmes_linux_64" 4) Genemark ".gm_key" Make sure that you have all four items directly under the data directory.root/source.sh -species=mysp -genome=genome.fa.masked -bam= -softmasking -gff3 -cores=20" In the following commands, you will download two Docker images from the Dockerhub.ĭocker1 run -rm -v /workdir/$USER/project2:/data biohpc/braker2 sh -c ". Detailed information about docker1 can be found at. The PASA image is provided by the software developer.įor security reasons, on the BioHPC system you need to run Docker through a wrapper "docker1", which is developed by Cornell Bioinformatics Facility. Detailed information about this image can be found at. When running the Braker2 pipeline, you need to put the GeneMark software directory and license file in the same directory as the input files. The Docker image of biohpc/braker2 is built by the BioHPC team, it includes all software required by the Braker2 pipeline, except the GeneMark-EX software and license files. But within a Docker container, you can run a different type of Linux, for example, Ubuntu. All BioHPC computers run CentOS Linux 7.5.
Perl change_path_in_perl_ "/usr/bin/env perl"ġ.4 Pull Docker images for Braker2 and PASA from the DockerhubĪ Docker image file is a template file that can be used to start a Docker container, an enclosed virtual Linux instance. #use the gmes_linux_64.tar.gz we provided, which is a version compatible with braker2 version in our docker container.
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