diff test-data.sh @ 2:69900ffd3b8e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data.sh	Mon Mar 16 08:22:08 2020 -0400
@@ -0,0 +1,58 @@
+#!/usr/bin/env bash
+
+# install conda
+if type conda > /dev/null; then  
+	true
+else
+	tmp=$(mktemp -d)
+	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+	bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
+	source "$tmp/miniconda/bin/activate"
+fi
+
+eval "$(conda shell.bash hook)"
+
+# install conda env
+if grep -Fq __bioconductor-dada2@1.14 <<< $(conda env list); then
+	true
+else
+	conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-dada2@1.14 bioconductor-dada2=1.14
+fi
+
+conda activate __bioconductor-dada2@1.14
+
+# create test data
+cd test-data/
+
+# download Mothur SOP data from zenodo (GTN), same as 
+# http://www.mothur.org/w/images/d/d6/MiSeqSOPData.zip but stable links
+# but file names need to be fixed
+wget -nc -O F3D0_S188_L001_R1_001.fastq https://zenodo.org/record/800651/files/F3D0_R1.fastq?download=1
+wget -nc -O F3D0_S188_L001_R2_001.fastq https://zenodo.org/record/800651/files/F3D0_R2.fastq?download=1
+wget -nc -O F3D141_S207_L001_R1_001.fastq https://zenodo.org/record/800651/files/F3D141_R1.fastq?download=1
+wget -nc -O F3D141_S207_L001_R2_001.fastq https://zenodo.org/record/800651/files/F3D141_R2.fastq?download=1
+
+# zip and reduce data to ~ 10% (for speed)
+for i in *fastq
+do
+	head -n 3000 "$i" | gzip -c > "$i.gz"
+done
+rm *fastq
+
+# download data bases from https://zenodo.org/record/158955
+# as mentioned in https://benjjneb.github.io/dada2/training.html
+wget -nc -O reference.fa.gz https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1
+wget -nc -O reference_species.fa.gz https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1
+
+# take ~ 5% of the reference (for speed)
+zcat reference.fa.gz | head -n 1000 | gzip -c > t && mv t reference.fa.gz
+zcat reference_species.fa.gz | head -n 1000 | gzip -c > t && mv t reference_species.fa.gz
+
+
+# generate outputs
+Rscript gentest.R
+
+conda deactivate
+
+# # remove files only needed for test generation
+# rm learnErrors_F3D0_R2.pdf dada_F3D0_R2.Rdata