Purdue University

Commands

• cactus
• cactus-align
• cactus-align-batch
• cactus-blast
• cactus-graphmap
• cactus-graphmap-join
• cactus-graphmap-split
• cactus-minigraph
• cactus-prepare
• cactus-prepare-toil
• cactus-preprocess
• cactus-refmap
• cactus2hal-stitch.sh
• cactus2hal.py
• cactusAPITests
• cactus_analyseAssembly
• cactus_barTests
• cactus_batch_mergeChunks
• cactus_chain
• cactus_consolidated
• cactus_covered_intervals
• cactus_fasta_fragments.py
• cactus_fasta_softmask_intervals.py
• cactus_filterSmallFastaSequences.py
• cactus_halGeneratorTests
• cactus_local_alignment.py
• cactus_makeAlphaNumericHeaders.py
• cactus_softmask2hardmask

Module

You can load the modules by:

module load biocontainers
module load cactus

Example job

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 Cactus on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cactus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cactus

wget https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt
cactus jobStore evolverMammals.txt evolverMammals.hal