Qiime2 on the Hoffman2 Cluster

A centralized installation of qiime2 is available via anaconda:

To run qiime2 interactively:

qrsh #any resource needed
module load anaconda3/2022.05
conda activate qiime2-2021.8

you can now test that things are working with:

qiime --help

to exit from the conda environment please use:

source deactivate

##### submit_qiime.sh SCRIPT START #######
#!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o joblog.$JOB_ID
#$ -j y
# RESOURCE REQUESTED (CHANGE THE NEXT TWO LINES AS NEEDED):
#$ -l h_rt=1:00:00,h_data=1G
#$ -pe shared 1
# Email address to notify
#$ -M $USER@mail
# Notify when
#$ -m bea

# echo job info on joblog:
echo "Job $JOB_ID started on: " `hostname -s`
echo "Job $JOB_ID started on: " `date `
echo " "

# load the job environment:
. /u/local/Modules/default/init/modules.sh

module load anaconda3/2022.05

conda activate qiime2-2021.8

# run qiime2 code, for example (CHANGE AS NEEDED):
echo 'qiime --help'
qiime --help

source deactivate

# echo job info on joblog:
echo "Job $JOB_ID ended on: " `hostname -s`
echo "Job $JOB_ID ended on: " `date `
echo " "
##### submit_qiime.sh SCRIPT END #######

echo 'qiime --help'
qiime --help

to reflect the actual qiime commands you intend to use.

# RESOURCE REQUESTED:
#$ -l h_rt=1:00:00,h_data=1G
#$ -pe shared 1

to reflect the time (h_rt), memory (h_data) and number of cores (shared X) you intend to use (you may also need to add to the "#$ -l" line the complex "highp" if you intend to run your code on your group resources (you would then use: "#$ -l h_rt=HHH:00:00,h_data=XG,highp").

When you are done editing the submission script issue:

chmod u+x submit_qiime2.sh

and you can then submit your job with:

qsub submit_qiime2.sh

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RD - October, 2017
RD - Last updated September 2022