Mcl
Introduction
Mcl is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs.
For more information, please check:
BioContainers: https://biocontainers.pro/tools/mcl
Home page: http://micans.org/mcl/
Note
Please follow the recommended citation guidelines from the developers when you use the tool in research.
Versions
Cluster |
Version(s) |
|---|---|
ANVIL |
14.137-pl5262 |
BELL |
14.137-pl5262 |
GAUTSCHI |
14.137-pl5262 |
NEGISHI |
14.137-pl5262 |
SCHOLAR |
14.137-pl5262 |
Commands
clm
clmformat
clxdo
mcl
mclblastline
mclcm
mclpipeline
mcx
mcxarray
mcxassemble
mcxdeblast
mcxdump
mcxi
mcxload
mcxmap
mcxrand
mcxsubs
Module
You can load the modules by:
module load biocontainers
module load mcl
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 mcl on our clusters:
#!/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=mcl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers mcl
# Your mcl workflow...
#!/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=mcl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers mcl
# Your mcl workflow...
#!/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=mcl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers mcl
# Your mcl workflow...
#!/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=mcl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers mcl
# Your mcl workflow...
#!/bin/bash
#SBATCH -A queue # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mcl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers mcl
# Your mcl workflow...