sepp
Link to section 'Introduction' of 'sepp' Introduction
Sepp stands for SATé-Enabled Phylogenetic Placement and addresses the problem of phylogenetic placement for meta-genomic short reads.
For more information, please check its website: https://biocontainers.pro/tools/sepp and its home page on Github.
Link to section 'Versions' of 'sepp' Versions
- 4.5.1
Link to section 'Commands' of 'sepp' Commands
- run_sepp.py
- run_upp.py
- split_sequences.py
- sumlabels.py
- sumtrees.py
Link to section 'Module' of 'sepp' Module
You can load the modules by:
module load biocontainers
module load sepp
Link to section 'Example job' of 'sepp' 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 Sepp on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sepp
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers sepp
run_sepp.py -t mock/rpsS/sate.tre \
-r mock/rpsS/sate.tre.RAxML_info \
-a mock/rpsS/sate.fasta \
-f mock/rpsS/rpsS.even.fas \
-o rpsS.out.default