BUpicrust

Implementation of PiCrust2 for SCC.

Accepts outputs from QIIME2 DADA2, as generated by the BU16s pipeline.

PiCrust 2 documentation: https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial

Set up

Add an environment variable to your ~/.bashrc. ONLY DO THIS ONCE!

echo "export BUpicrust=/projectnb/talbot-lab-data/msilver/BUpicrust" >> ~/.bashrc
source ~/.bashrc

See input arguments with python create_inputs.py -h

Tutorial

First, complete the BU16s tutorial, at least through the DADA2 steps for generating ASVs.

Then create an input parameters file for BUpicrust with (this assumes you used --output_dir $BU16s/test for BU16s):

python $BUpicrust/create_inputs.py \
    --biom $BU16s/test/intermediate/dada2/table.qza \
    --seqs $BU16s/test/intermediate/dada2/representative_sequences.qza \
    --outdir $BU16s/test \
    --paramout TEST_INPUTS.sh

Your inputs file should look like picrust_test.sh

Then submit the batch job with:

qsub -P <BU PROJECT NAME> $BUpicrust/picrust.qsub picrust_test.sh