teambraker/braker3 repository overview

⁠BRAKER3

BRAKER1, BRAKER2, and BRAKER3 are a genome annotation software suite that is here made available via a Docker container. Further information on BRAKER is available at https://github.com/Gaius-Augustus/BRAKER⁠

This Docker image, which is suiltable for buiding a Singularity image as well, contains BRAKER3 including dependencies.

⁠Using this container

For running the Docker container shell, run as follows (we have never tested it with Docker and at this point in time):

sudo docker run --user 1000:100 --rm -it teambraker/braker3:latest bash

For rendering JupyterNotebooks from BRAKER workshops, run the Docker container as follows:

sudo docker run --rm -it -u 1000:0 -p 8888:8888 teambraker/braker3:latest

For Singularity, build the sif-file as follows:

singularity build braker3.sif docker://teambraker/braker3:latest

Execute BRAKER like this (i.e. it automatically mounts the user's home directory on the host system):

singularity exec braker3.sif braker.pl

We provide 3 test scripts for the singularity container. They can be copied to the host as follows:

singularity exec -B $PWD:$PWD braker3.sif cp /opt/BRAKER/example/singularity-tests/test1.sh .
singularity exec -B $PWD:$PWD braker3.sif cp /opt/BRAKER/example/singularity-tests/test2.sh .
singularity exec -B $PWD:$PWD braker3.sif cp /opt/BRAKER/example/singularity-tests/test3.sh .

They can be executed with bash. Prior running them, you need to export two bash environment variables on the host:

export BRAKER_SIF=/your/path/to/braker3.sif

After that, execute with:

bash test1.sh # tests BRAKER1
bash test2.sh # tests BRAKER2
bash test3.sh # tests BRAKER3

The container does not contain the OrthoDB partitions that are required as input for BRAKER2 and BRAKER3. You can download the respective file for your clade from https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11/index.html⁠ .

If you have never used Singularity, before: by default (if you do not use -B $PWD:$PWD option), it mounts your home directory. It can therefore see all files, there. You can instead mount your current working directory with `-B $PWD:$PWD' , or any other directory of your liking. The container always sees your home directory (this is important because the GeneMark-ETP license key needs to reside in your home directory).

⁠Software contained in this container

• GeneMark-ETP (Creative Commons Attribution NonCommercial ShareAlike 4.0n license)
• Ubuntu 22.04 (jammy), all legal terms on Ubuntu are available at https://ubuntu.com/legal⁠
• Ubuntu packages: bzip2, ca-certificates, fonts-liberation, locales, pandoc, tini, wget, htop, openssh-client, vim, rsync, git, nano-tiny , tzdata, unzip, vim-tiny, less, texlive-xetex, texlive-fonts-recommended, texlive-plain-generic, build-essential, cm-super, dvipng, ffmpeg, time, man-db, g++, less, zlib1g-dev, augustus, augustus-data, augustus-doc, libyaml-perl, libhash-merge-perl, libparallel-forkmanager-perl, libscalar-util-numeric-perl, libclass-data-inheritable-perl, libexception-class-perl, libtest-pod-perl, libfile-which-perl, libmce-perl, libthread-queue-perl, libmath-utils-perl, libscalar-list-utils-perl, bedtools, bamtools
• Micromamba (https://github.com/mamba-org/mamba#micromamba⁠), BSD 3-Clause "New" or "Revised" License at https://github.com/mamba-org/mamba/blob/main/LICENSE⁠
• Conda/mamba packages: nbresuse, jupyter-starters, biopython
• Jupyter labextensions: jupyterlab-topbar-extension jupyterlab-system-monitor
• GeneMark-ETP v.0.0.1 5 fix version number, license at /opt/ETP+/lincense.txt
• Seqstats from https://github.com/clwgg/seqstats⁠ , MIT License at /opt/seqsats/LICENSE
• HISAT2 from https://github.com/DaehwanKimLab/hisat2⁠ , GNU General Public License v3.0 at /opt/hisat2/LICENSE
• CDB fasta tools from https://github.com/gpertea/cdbfasta⁠ , Artistic License 2.0 at https://opensource.org/licenses/artistic-license-2.0⁠
• StringTie2 v.2.2.1 from http://ccb.jhu.edu/software/stringtie/dl/stringtie-2.2.1.Linux_x86_64.tar.gz⁠, Artistic License 2.0 at /opt/stringtie-2.2.1.Linux_x86_64/LICENSE
• GffRead from https://github.com/gpertea/gffread⁠ , MIT License at /opt/gffread/LICENSE
• DIAMOND v2.0.15 from http://github.com/bbuchfink/diamond⁠ , GNU General Public License v3.0 at /opt/diamond/LICENSE
• TSEBRA from https://github.com/Gaius-Augustus/TSEBRA⁠ , Artistic License 2.0 at https://opensource.org/licenses/Artistic-2.0⁠
• MakeHub from https://github.com/Gaius-Augustus/MakeHub⁠ , GNU General Public License v3.0 at /opt/MakeHub/LICENSE
• UCSC Tools bedToBigBed, genePredCheck, faToTwoBit, gtfToGenePred, hgGcPercent, ixIxx, twoBitInfo, wigToBigWig, genePredToBed, genePredToBigGenePred , License of UC Regents at https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/LICENSE⁠ % katharina must put that license into the container
• BRAKER from https://github.com/Gaius-Augustus/BRAKER⁠ , Artistic License 1.0 at /opt/BRAKER/LICENSE.txt
• sratoolkit from https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz⁠ , Public Domain Notice at https://github.com/ncbi/sra-tools/blob/master/LICENSE⁠

⁠Authors & Contact

The Docker file for this container was created by Stefan Kemnitz and Katharina Hoff at University of Greifswald.

BRAKER3 is authored by Lars Gabriel, Tomas Bruna, Simone Lange, Alexandre Lomsadze, Katharina Hoff, Mario Stanke, and Mark Borodovsky.

For questions about this container, please contact [email protected]⁠