.. _backbone-label: Bedops ============================== Introduction ~~~~~~~~ Bedops is a software package for manipulating and analyzing genomic interval data. | For more information, please check: | BioContainers: https://biocontainers.pro/tools/bedops | Home page: https://bedops.readthedocs.io/en/latest/ .. note:: Please follow the recommended citation guidelines from the developers when you use the tool in research. Versions ~~~~~~~ .. list-table:: :width: 100 % :widths: 25 75 :header-rows: 1 * - Cluster - Version(s) * - ANVIL - 2.4.39 * - BELL - 2.4.39 * - GAUTSCHI - 2.4.39 * - NEGISHI - 2.4.39 * - SCHOLAR - 2.4.39 Commands ~~~~~~~ - bam2bed - bam2bed-float128 - bam2bed_gnuParallel - bam2bed_gnuParallel-float128 - bam2bed_gnuParallel-megarow - bam2bed_gnuParallel-typical - bam2bed-megarow - bam2bed_sge - bam2bed_sge-float128 - bam2bed_sge-megarow - bam2bed_sge-typical - bam2bed_slurm - bam2bed_slurm-float128 - bam2bed_slurm-megarow - bam2bed_slurm-typical - bam2bed-typical - bam2starch - bam2starch-float128 - bam2starch_gnuParallel - bam2starch_gnuParallel-float128 - bam2starch_gnuParallel-megarow - bam2starch_gnuParallel-typical - bam2starch-megarow - bam2starch_sge - bam2starch_sge-float128 - bam2starch_sge-megarow - bam2starch_sge-typical - bam2starch_slurm - bam2starch_slurm-float128 - bam2starch_slurm-megarow - bam2starch_slurm-typical - bam2starch-typical - bedextract - bedextract-float128 - bedextract-megarow - bedextract-typical - bedmap - bedmap-float128 - bedmap-megarow - bedmap-typical - bedops - bedops-float128 - bedops-megarow - bedops-typical - closest-features - closest-features-float128 - closest-features-megarow - closest-features-typical - convert2bed - convert2bed-float128 - convert2bed-megarow - convert2bed-typical - gff2bed - gff2bed-float128 - gff2bed-megarow - gff2bed-typical - gff2starch - gff2starch-float128 - gff2starch-megarow - gff2starch-typical - gtf2bed - gtf2bed-float128 - gtf2bed-megarow - gtf2bed-typical - gtf2starch - gtf2starch-float128 - gtf2starch-megarow - gtf2starch-typical - gvf2bed - gvf2bed-float128 - gvf2bed-megarow - gvf2bed-typical - gvf2starch - gvf2starch-float128 - gvf2starch-megarow - gvf2starch-typical - psl2bed - psl2bed-float128 - psl2bed-megarow - psl2bed-typical - psl2starch - psl2starch-float128 - psl2starch-megarow - psl2starch-typical - rmsk2bed - rmsk2bed-float128 - rmsk2bed-megarow - rmsk2bed-typical - rmsk2starch - rmsk2starch-float128 - rmsk2starch-megarow - rmsk2starch-typical - sam2bed - sam2bed-float128 - sam2bed-megarow - sam2bed-typical - sam2starch - sam2starch-float128 - sam2starch-megarow - sam2starch-typical - sort-bed - sort-bed-float128 - sort-bed-megarow - sort-bed-typical - starch - starchcat - starchcat-float128 - starchcat-megarow - starchcat-typical - starchcluster_gnuParallel - starchcluster_gnuParallel-float128 - starchcluster_gnuParallel-megarow - starchcluster_gnuParallel-typical - starchcluster_sge - starchcluster_sge-float128 - starchcluster_sge-megarow - starchcluster_sge-typical - starchcluster_slurm - starchcluster_slurm-float128 - starchcluster_slurm-megarow - starchcluster_slurm-typical - starch-diff - starch-diff-float128 - starch-diff-megarow - starch-diff-typical - starch-float128 - starch-megarow - starchstrip - starchstrip-float128 - starchstrip-megarow - starchstrip-typical - starch-typical - switch-BEDOPS-binary-type - unstarch - unstarch-float128 - unstarch-megarow - unstarch-typical - update-sort-bed-migrate-candidates - update-sort-bed-migrate-candidates-float128 - update-sort-bed-migrate-candidates-megarow - update-sort-bed-migrate-candidates-typical - update-sort-bed-slurm - update-sort-bed-slurm-float128 - update-sort-bed-slurm-megarow - update-sort-bed-slurm-typical - update-sort-bed-starch-slurm - update-sort-bed-starch-slurm-float128 - update-sort-bed-starch-slurm-megarow - update-sort-bed-starch-slurm-typical - vcf2bed - vcf2bed-float128 - vcf2bed-megarow - vcf2bed-typical - vcf2starch - vcf2starch-float128 - vcf2starch-megarow - vcf2starch-typical - wig2bed - wig2bed-float128 - wig2bed-megarow - wig2bed-typical - wig2starch - wig2starch-float128 - wig2starch-megarow - wig2starch-typical Module ~~~~~~~~ You can load the modules by:: module load biocontainers module load bedops Example job ~~~~~ .. warning:: Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead. To run bedops on our clusters: .. tab-set:: .. tab-item:: Anvil .. code-block:: bash #!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -p wholenode # Partition name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=bedops #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers bedops # Your bedops workflow... .. tab-item:: Bell, Gautschi, or Negishi .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p cpu # Partition name #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=bedops #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers bedops # Your bedops workflow... .. tab-item:: Gautschi-AI .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p ai # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=bedops #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers bedops # Your bedops workflow... .. tab-item:: Gilbreth .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p a100 # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH --mem=2G # Memory #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=bedops #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers bedops # Your bedops workflow... .. tab-item:: Scholar .. code-block:: bash #!/bin/bash #SBATCH -A queue # Queue name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=bedops #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers bedops # Your bedops workflow...