Qiime/Qiime2 on the Hoffman2 cluster
A centralized installation of qiime2 is available via anaconda:
To run:
check which versions are available with:
and load the needed environment. For example for qiime2-2018.2 you can do so with:
you can now test that things are working with:
to exit from the conda environment please use:
To run qiime2 interactively:
To use qiime2 from a batch job you will need to create a script, called for example submit_qiime.sh, that has these commands in it:
##### SUBMIT QIIME2 SCRIPT START #######
#!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o joblog.$JOB_ID
#$ -j y
# RESOURCE REQUESTED:
#$ -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 anaconda
source activate qiime2-2017.9
# run qiime2 code, for example:
echo 'qiime --help'
qiime --help
source deactivate
# echo job info on joblog:
echo "Job $JOB_ID ended on: " `hostname -s`
echo "Job $JOB_ID ended on: " `date `
echo " "
##### SUBMIT QIIME2 SCRIPT END #######
Please change:
to reflect the actual qiime commands you intend to use.
Also please change:
to reflect the time (h_rt), memory (h_data) and number of cores (shared X) you intend to use (you may also need to add to the "#$ -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:
and you can then submit your job with:
__
RD - October, 2017
RD - Last updated March 2018
To run:
qrsh
module load anaconda
check which versions are available with:
conda info -e
and load the needed environment. For example for qiime2-2018.2 you can do so with:
source activate qiime2-2017.9
you can now test that things are working with:
qiime --help
to exit from the conda environment please use:
source deactivate
To run qiime2 interactively:
qrsh
module load anaconda
source activate qiime2-2017.9
<qiime2 commands>
source deactivate
To use qiime2 from a batch job you will need to create a script, called for example submit_qiime.sh, that has these commands in it:
##### SUBMIT QIIME2 SCRIPT START #######
#!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o joblog.$JOB_ID
#$ -j y
# RESOURCE REQUESTED:
#$ -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 anaconda
source activate qiime2-2017.9
# run qiime2 code, for example:
echo 'qiime --help'
qiime --help
source deactivate
# echo job info on joblog:
echo "Job $JOB_ID ended on: " `hostname -s`
echo "Job $JOB_ID ended on: " `date `
echo " "
##### SUBMIT QIIME2 SCRIPT END #######
Please change:
# run qiime2 code, for example:
echo 'qiime --help'
qiime --help
to reflect the actual qiime commands you intend to use.
Also please change:
# RESOURCE REQUESTED:
#$ -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
__
RD - October, 2017
RD - Last updated March 2018