Mercurial > repos > iuc > dada2_assigntaxonomyaddspecies

annotate test-data.sh @ 2:1c9715cef808 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
author iuc
date Mon, 16 Mar 2020 08:03:24 -0400
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1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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1 #!/usr/bin/env bash
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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2
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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3 # install conda
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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4 if type conda > /dev/null; then
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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5 true
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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6 else
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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7 tmp=$(mktemp -d)
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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8 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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9 bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
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10 source "$tmp/miniconda/bin/activate"
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11 fi
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1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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13 eval "$(conda shell.bash hook)"
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14
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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15 # install conda env
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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16 if grep -Fq __bioconductor-dada2@1.14 <<< $(conda env list); then
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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17 true
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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18 else
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19 conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-dada2@1.14 bioconductor-dada2=1.14
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20 fi
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1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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22 conda activate __bioconductor-dada2@1.14
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1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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24 # create test data
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25 cd test-data/
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26
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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27 # download Mothur SOP data from zenodo (GTN), same as
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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28 # http://www.mothur.org/w/images/d/d6/MiSeqSOPData.zip but stable links
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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29 # but file names need to be fixed
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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30 wget -nc -O F3D0_S188_L001_R1_001.fastq https://zenodo.org/record/800651/files/F3D0_R1.fastq?download=1
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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31 wget -nc -O F3D0_S188_L001_R2_001.fastq https://zenodo.org/record/800651/files/F3D0_R2.fastq?download=1
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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32 wget -nc -O F3D141_S207_L001_R1_001.fastq https://zenodo.org/record/800651/files/F3D141_R1.fastq?download=1
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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33 wget -nc -O F3D141_S207_L001_R2_001.fastq https://zenodo.org/record/800651/files/F3D141_R2.fastq?download=1
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1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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35 # zip and reduce data to ~ 10% (for speed)
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36 for i in *fastq
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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37 do
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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38 head -n 3000 "$i" | gzip -c > "$i.gz"
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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39 done
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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40 rm *fastq
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1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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42 # download data bases from https://zenodo.org/record/158955
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43 # as mentioned in https://benjjneb.github.io/dada2/training.html
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44 wget -nc -O reference.fa.gz https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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45 wget -nc -O reference_species.fa.gz https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1
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46
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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47 # take ~ 5% of the reference (for speed)
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48 zcat reference.fa.gz | head -n 1000 | gzip -c > t && mv t reference.fa.gz
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49 zcat reference_species.fa.gz | head -n 1000 | gzip -c > t && mv t reference_species.fa.gz
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1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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51
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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52 # generate outputs
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53 Rscript gentest.R
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54
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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55 conda deactivate
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56
1c9715cef808 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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57 # # remove files only needed for test generation
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58 # rm learnErrors_F3D0_R2.pdf dada_F3D0_R2.Rdata