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scidap-qiime2-Dockerfile
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#################################################################
# Dockerfile
#
# Software: QIIME2
# Software Version: v2023.5
# Description: Dockerized version of QIIME2 workflow
# Website: https://github.com/datirium/workflows
# Provides: R script to run QIIME2 platform
# Base Image: quay.io/qiime2/core:2023.5
# Build Cmd: docker build --platform linux/amd64 --no-cache --rm -t qiime2-dev -f scidap-qiime2-Dockerfile . > ~/Desktop/dockerbuild.log 2>&1
# Run Cmd: docker run --rm -ti qiime2-dev /bin/bash
# Push Cmd1: docker tag qiime2-dev robertplayer/scidap-qiime2:stable
# Cmd2: docker image push robertplayer/scidap-qiime2:stable
# Pull Cmd: docker pull robertplayer/scidap-qiime2:stable
# Test Stable: docker run --rm -ti robertplayer/scidap-qiime2:stable /bin/bash
# re-tag for PR: docker tag qiime2-dev robertplayer/scidap-qiime2:v1.0.0
# Push for PR: docker image push robertplayer/scidap-qiime2:v1.0.0
#
# NOTES:
#
#################################################################
### Base Image
# use for initial image build
FROM quay.io/qiime2/core:2023.5
# use for small script updates etc (shorter build time from stable)
#FROM robertplayer/scidap-qiime2:stable
LABEL maintainer="robert.player@datirium.com"
ENV DEBIAN_FRONTEND noninteractive
################## BEGIN INSTALLATION ######################
WORKDIR /tmp
COPY ./scripts/run_qiime2_sample_pe.sh /usr/local/bin/
COPY ./scripts/run_qiime2_aggregate.sh /usr/local/bin/
COPY ./scripts/transpose_tsv.awk /usr/local/bin/
### Installing dependencies
RUN apt-get update && \
### Installing R dependencies
# R -e 'install.packages("ggplot2", repo = "https://cloud.r-project.org/")' && \
# R -e 'install.packages("BiocManager", repo = "https://cloud.r-project.org/")' && \
# R -e 'BiocManager::install("RnBeads.rn5")' && \
### Installing scripts/data
mkdir -p /dockerdata && \
wget -O "/dockerdata/gg_2022_10_backbone_full_length.nb.qza" "https://data.qiime2.org/classifiers/greengenes/gg_2022_10_backbone_full_length.nb.qza" && \
chmod +x /usr/local/bin/run_qiime2_sample_pe.sh && \
ls -la /usr/local/bin/run_qiime2_sample_pe.sh && \
chmod +x /usr/local/bin/run_qiime2_aggregate.sh && \
ls -la /usr/local/bin/run_qiime2_aggregate.sh && \
chmod +x /usr/local/bin/transpose_tsv.awk && \
ls -la /usr/local/bin/transpose_tsv.awk && \
### Cleaning
apt-get clean && \
apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc/* && \
strip /usr/local/bin/*; true