Run the MVP tutorial for q2 2017.2.0 using q2-deblur

q2-2017.2.0.mvp.sh

#!/bin/bash
set -e
set -x

envname=q2deblur_mvp_test
executiondir=mvp
redeploy=$1

source deactivate

curl=/usr/bin/curl  # to circumvent the conda install

if [[ ${redeploy} == "redeploy" ]];
then
    if [[ $(conda env list | grep -c ${envname}) == 1 ]];
    then
        conda env remove -y --name ${envname}
    fi

    if [[ $(uname) == "Darwin" ]];
    then
        reqs=https://data.qiime2.org/distro/core/qiime2-2017.2-conda-osx-64.txt
    else
        reqs=https://data.qiime2.org/distro/core/qiime2-2017.2-conda-linux-64.txt
    fi

    conda create -y --name ${envname} --file ${reqs}
    source activate ${envname}
    conda install -y -c bioconda VSEARCH==2.0.3 MAFFT==7.221 SortMeRNA==2.0 biom-format
    pip install deblur==1.0.0
    pip install https://github.com/wasade/q2-deblur/archive/master.zip
else
    source activate ${envname}
fi

if [[ -d ${executiondir} ]];
then
    echo "${executiondir} already exists"
    exit 1
else
    mkdir ${executiondir}
fi

pushd ${executiondir} > /dev/null

${curl} -sL "https://data.qiime2.org/2017.2/tutorials/moving-pictures/sample_metadata.tsv" > "sample-metadata.tsv"

mkdir emp-single-end-sequences
${curl} -sL "https://data.qiime2.org/2017.2/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz" > "emp-single-end-sequences/barcodes.fastq.gz"
${curl} -sL "https://data.qiime2.org/2017.2/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz" > "emp-single-end-sequences/sequences.fastq.gz"

qiime tools import --type EMPSingleEndSequences --input-path emp-single-end-sequences --output-path emp-single-end-sequences.qza

qiime demux emp-single --i-seqs emp-single-end-sequences.qza --m-barcodes-file sample-metadata.tsv --m-barcodes-category BarcodeSequence --o-per-sample-sequences demux.qza
qiime demux summarize --i-data demux.qza --o-visualization demux.qzv

qiime deblur denoise-16S --i-demultiplexed-seqs demux.qza --p-trim-length 100 --o-representative-sequences rep-seqs --o-table table

# qiime dada2 plot-qualities --i-demultiplexed-seqs demux.qza --o-visualization demux-qual-plots --p-n 10
# qiime dada2 denoise --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 100 --o-representative-sequences rep-seqs --o-table table

qiime feature-table summarize --i-table table.qza --o-visualization table --m-sample-metadata-file sample-metadata.tsv
qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs

qiime alignment mafft --i-sequences rep-seqs.qza --o-alignment aligned-rep-seqs

qiime alignment mask --i-alignment aligned-rep-seqs.qza --o-masked-alignment masked-aligned-rep-seqs

qiime phylogeny fasttree --i-alignment masked-aligned-rep-seqs.qza --o-tree unrooted-tree
qiime phylogeny midpoint-root --i-tree unrooted-tree.qza --o-rooted-tree rooted-tree

qiime diversity core-metrics --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 1441 --output-dir cm1441

qiime diversity alpha-group-significance --i-alpha-diversity cm1441/faith_pd_vector.qza --m-metadata-file sample-metadata.tsv  --o-visualization cm1441/faith-pd-group-significance
qiime diversity alpha-group-significance --i-alpha-diversity cm1441/evenness_vector.qza --m-metadata-file sample-metadata.tsv  --o-visualization cm1441/evenness-group-significance

qiime diversity alpha-correlation --i-alpha-diversity cm1441/faith_pd_vector.qza --m-metadata-file sample-metadata.tsv  --o-visualization cm1441/faith-pd-correlation
qiime diversity alpha-correlation --i-alpha-diversity cm1441/evenness_vector.qza --m-metadata-file sample-metadata.tsv  --o-visualization cm1441/evenness-correlation

qiime diversity beta-group-significance --i-distance-matrix cm1441/unweighted_unifrac_distance_matrix.qza --m-metadata-file sample-metadata.tsv --m-metadata-category BodySite --o-visualization cm1441/unweighted-unifrac-body-site-significance
qiime diversity beta-group-significance --i-distance-matrix cm1441/unweighted_unifrac_distance_matrix.qza --m-metadata-file sample-metadata.tsv --m-metadata-category Subject --o-visualization cm1441/unweighted-unifrac-subject-group-significance

qiime diversity bioenv --i-distance-matrix cm1441/unweighted_unifrac_distance_matrix.qza --m-metadata-file sample-metadata.tsv --o-visualization cm1441/unweighted-unifrac-bioenv
qiime diversity bioenv --i-distance-matrix cm1441/bray_curtis_distance_matrix.qza --m-metadata-file sample-metadata.tsv --o-visualization cm1441/bray-curtis-bioenv

qiime emperor plot --i-pcoa cm1441/unweighted_unifrac_pcoa_results.qza --o-visualization cm1441/unweighted-unifrac-emperor --m-metadata-file sample-metadata.tsv --p-custom-axis DaysSinceExperimentStart
qiime emperor plot --i-pcoa cm1441/bray_curtis_pcoa_results.qza --o-visualization cm1441/bray-curtis-emperor --m-metadata-file sample-metadata.tsv --p-custom-axis DaysSinceExperimentStart

${curl} -sL "https://data.qiime2.org/2017.2/common/gg-13-8-99-515-806-nb-classifier.qza" > "gg-13-8-99-515-806-nb-classifier.qza"

qiime feature-classifier classify --i-classifier gg-13-8-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy

qiime taxa tabulate --i-data taxonomy.qza --o-visualization taxonomy
qiime taxa barplot --i-table table.qza --i-taxonomy taxonomy.qza --m-metadata-file sample-metadata.tsv --o-visualization taxa-bar-plots

qiime composition add-pseudocount --i-table table.qza --o-composition-table comp-table
qiime composition ancom --i-table comp-table.qza --m-metadata-file sample-metadata.tsv --m-metadata-category BodySite --o-visualization ancom-BodySite

qiime taxa collapse --i-table table.qza --i-taxonomy taxonomy.qza --p-level 2 --o-collapsed-table table-l2

qiime composition add-pseudocount --i-table table-l2.qza --o-composition-table comp-table-l2
qiime composition ancom --i-table comp-table-l2.qza --m-metadata-file sample-metadata.tsv --m-metadata-category BodySite --o-visualization l2-ancom-BodySite

popd > /dev/null