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=== Using Singularity === | === Using Singularity === | ||
The QIIME2 developers publish images on [https:// | 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 [[Singularity/en#Creating_an_image_using_Docker_Hub|build a Singularity image]]: | ||
{{Commands | {{Commands | ||
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}} | }} | ||
This build step may take over an hour, but you only need do this once. | 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. | ||
for later re-use. | |||
Then run your code as described at [[Singularity]]. Typically you will run each QIIME command in a <code>singularity exec</code> statement: | Then run your code as described at [[Singularity]]. Typically you will run each QIIME command in a <code>singularity exec</code> statement: | ||
{{Commands | {{Commands | ||
|singularity exec qiime2- | |singularity exec qiime2-2021.11.sif <your QIIME command> | ||
}} | }} | ||
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singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | ||
-B /projects/someuser/path/to/inputs:/inputs qiime2- | -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]' \ | ||
--input-path /inputs/some_fastafile.fa \ | --input-path /inputs/some_fastafile.fa \ | ||
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singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | ||
-B /projects/someuser/path/to/inputs:/inputs qiime2- | -B /projects/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \ | ||
qiime tools import \ | qiime tools import \ | ||
--type 'FeatureData[Taxonomy]' \ | --type 'FeatureData[Taxonomy]' \ | ||
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singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | ||
-B /projects/someuser/path/to/inputs:/inputs qiime2- | -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 \ | ||
--i-reference-reads /outputs/some_output_feature.qza \ | --i-reference-reads /outputs/some_output_feature.qza \ | ||
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{{Commands | {{Commands | ||
|export TZ{{=}}'UTC' | |export TZ{{=}}'UTC' | ||
|singularity exec qiime2- | |singularity exec qiime2-2021.11.sif qiime tools import ... | ||
}} | }} | ||
=References = | =References = | ||