cactus
Link to section 'Introduction' of 'cactus' Introduction
Cactus is a reference-free whole-genome multiple alignment program.
For more information, please check its website: https://biocontainers.pro/tools/cactus and its home page on Github.
Link to section 'Versions' of 'cactus' Versions
- 2.0.5
- 2.2.1
- 2.2.3-gpu
- 2.2.3
- 2.4.0-gpu
- 2.4.0
- 2.5.2
- 2.6.5
Link to section 'Commands' of 'cactus' 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
Link to section 'Module' of 'cactus' Module
You can load the modules by:
module load biocontainers
module load cactus
Link to section 'Example job' of '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