Irods
Introduction
iCommands is a collection of commands used to interact with an iRODS server
For more information, please check:
BioContainers: https://biocontainers.pro/tools/irods-icommands
Home page: https://irods.org/
Note
Please follow the recommended citation guidelines from the developers when you use the tool in research.
Versions
Cluster |
Version(s) |
|---|---|
ANVIL |
4.0.3 |
Commands
iadmin
ibun
icd
ichksum
ichmod
icp
ienv
ierror
iexecmd
iexit
ifsck
iget
igroupadmin
ihelp
iinit
ils
ilsresc
imcoll
imeta
imiscsvrinfo
imkdir
imv
ipasswd
iphybun
iphymv
ips
iput
ipwd
iqdel
iqmod
iqstat
iquest
iquota
ireg
irepl
irm
irmdir
irmtrash
irsync
irule
iscan
isysmeta
iticket
itrim
iuserinfo
ixmsg
izonereport
Module
You can load the modules by:
module load biocontainers
module load irods
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 irods 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=irods
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers irods
# Your irods 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=irods
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers irods
# Your irods 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=irods
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers irods
# Your irods 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=irods
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers irods
# Your irods workflow...
#!/bin/bash
#SBATCH -A queue # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=irods
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
module biocontainers irods
# Your irods workflow...