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QIIME/en: Difference between revisions
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== QIIME2 as a module == | == QIIME2 as a module == | ||
QIIME2 is now available in our environment using a module which wraps around a container. | QIIME2 is now available in our environment using a module which wraps around a container. To know which versions are available, run | ||
{{Command|module spider qiime2}} | {{Command|module spider qiime2}} | ||
After loading the module, you can run | After loading the module, you can run | ||
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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 | Then run your code as described in the [[Apptainer]] page. You will typically run each QIIME command in a <code>apptainer exec</code> statement: | ||
{{Commands | {{Commands | ||
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</pre> | </pre> | ||
Note that it is important to use the [[Apptainer#Bind_mounts|bind]] option (<code>-B</code>) with each folder you want to work with when you run programs in your container. For more information about Apptainer, you can watch | Note that it is important to use the [[Apptainer#Bind_mounts|bind]] option (<code>-B</code>) with each folder you want to work with when you run programs in your container. For more information about Apptainer, you can watch this [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: | ||