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QIIME/en: Difference between revisions
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Updating to match new version of source page
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#SBATCH --account=def-someuser | #SBATCH --account=def-someuser | ||
singularity exec -B /home -B / | singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | ||
qiime tools import | -B /projects/someuser/path/to/inputs:/inputs qiime2-2019.10.sif \ | ||
qiime tools import --type 'FeatureData[Sequence]' \ | |||
--input-path / | --input-path /inputs/some_fastafile.fa \ | ||
--output-path / | --output-path /outputs/some_output_feature.qza | ||
singularity exec -B /home -B / | singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | ||
-B /projects/someuser/path/to/inputs:/inputs qiime2-2019.10.sif \ | |||
qiime tools import \ | qiime tools import \ | ||
--type 'FeatureData[Taxonomy]' \ | --type 'FeatureData[Taxonomy]' \ | ||
--input-format HeaderlessTSVTaxonomyFormat \ | --input-format HeaderlessTSVTaxonomyFormat \ | ||
--input-path / | --input-path /inputs/some_taxonomy_file.tax \ | ||
--output-path / | --output-path /outputs/some_output_ref-taxonomy.qza | ||
singularity exec -B /home -B / | singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \ | ||
-B /projects/someuser/path/to/inputs:/inputs qiime2-2019.10.sif \ | |||
qiime feature-classifier fit-classifier-naive-bayes \ | qiime feature-classifier fit-classifier-naive-bayes \ | ||
--i-reference-reads / | --i-reference-reads /outputs/some_output_feature.qza \ | ||
--i-reference-taxonomy / | --i-reference-taxonomy /outputs/some_output_ref-taxonomy.qza \ | ||
--o-classifier / | --o-classifier /outputs/some_output_classifier.qza | ||
</pre> | </pre> | ||