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==Installation == | ==Installation == | ||
QIIME2 can be installed using [[ | QIIME2 can be installed using [[Apptainer]] or using EasyBuild. Apptainer is strongly preferred since it does not generate many thousands of files in your home directory, potentially causing you to exceed the disk quota limit on the number of files. | ||
=== Using | === Using Apptainer === | ||
The QIIME2 developers publish images on [https://quay.io/organization/qiime2 Quay.io]. In order to use one of these images on our systems you must first [[ | The QIIME2 developers publish images on [https://quay.io/organization/qiime2 Quay.io]. In order to use one of these images on our systems you must first [[Apptainer/en#Creating_an_image_using_Docker_Hub|build an Apptainer image]]: | ||
{{Commands | {{Commands | ||
|module load | |module load apptainer | ||
| | |apptainer build qiime2-2021.11.sif docker://quay.io/qiime2/core:2021.11 | ||
}} | }} | ||
This build step may take over an hour, but you only need to do this once. Save the image file (<code>qiime2-2021.11.sif</code> in this example) for later re-use. | This build step may take over an hour, but you only need to do this once. Save the image file (<code>qiime2-2021.11.sif</code> in this example) for later re-use. | ||
Then run your code as described at [[ | Then run your code as described at [[Apptainer]]. Typically you will run each QIIME command in a <code>apptainer exec</code> statement: | ||
{{Commands | {{Commands | ||
| | |apptainer exec qiime2-2021.11.sif <your QIIME command> | ||
}} | }} | ||
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#SBATCH --account=def-someuser | #SBATCH --account=def-someuser | ||
apptainer exec -B $PWD:/home -B /scratch/someuser:/outputs \ | |||
-B /projects/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \ | -B /projects/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \ | ||
qiime tools import --type 'FeatureData[Sequence]' \ | qiime tools import --type 'FeatureData[Sequence]' \ | ||
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--output-path /outputs/some_output_feature.qza | --output-path /outputs/some_output_feature.qza | ||
apptainer exec -B $PWD:/home -B /scratch/someuser:/outputs \ | |||
-B /projects/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \ | -B /projects/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \ | ||
qiime tools import \ | qiime tools import \ | ||
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--output-path /outputs/some_output_ref-taxonomy.qza | --output-path /outputs/some_output_ref-taxonomy.qza | ||
apptainer exec -B $PWD:/home -B /scratch/someuser:/outputs \ | |||
-B /projects/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \ | -B /projects/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \ | ||
qiime feature-classifier fit-classifier-naive-bayes \ | qiime feature-classifier fit-classifier-naive-bayes \ | ||
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</pre> | </pre> | ||
Note that it is important to use the [[ | Note that it is important to use the [[Apptainer#Bind_mounts|bind]] option (<tt>-B</tt>) with each folder you want to work with when you run programs in your container. For more information about Apptainer, you can watch the recorded [https://www.youtube.com/watch?v=bpmrfVqBowY Apptainer webinar]. | ||
On first importing data into QIIME format you may receive an error ending with a message like this: | On first importing data into QIIME format you may receive an error ending with a message like this: | ||
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Timezone offset does not match system offset: 0 != -18000. Please, check your config files. | Timezone offset does not match system offset: 0 != -18000. Please, check your config files. | ||
</pre> | </pre> | ||
This can be worked around by setting a time zone before invoking | This can be worked around by setting a time zone before invoking Apptainer: | ||
{{Commands | {{Commands | ||
|export TZ{{=}}'UTC' | |export TZ{{=}}'UTC' | ||
| | |apptainer exec qiime2-2021.11.sif qiime tools import ... | ||
}} | }} | ||