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[Work in progress!] Docker configuration for genomics workshop #44

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36 changes: 36 additions & 0 deletions Dockerfile
Original file line number Diff line number Diff line change
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FROM ubuntu:17.10
LABEL author="Daniel Standage"
LABEL maintainer="[email protected]"

WORKDIR /datacarpentry/
COPY ./bashrc /datacarpentry/.bashrc

# Precise versions not necessary for system packages
RUN apt-get update
RUN apt-get install -y less perl curl wget tmux nano

# We want precise versions for bioinformatics packages
RUN apt-get install -y \
fastqc=0.11.5+dfsg-6 \
trimmomatic=0.36+dfsg-3 \
bwa=0.7.15-5 \
samtools=1.4.1-1build1 \
bcftools=1.4.1-3build1

# Download and store some data sets
RUN mkdir -p /datacarpentry/.rawdata/
RUN curl -L https://osf.io/d98sh/?download=1 > /datacarpentry/.rawdata/SRR2584858_1.fastq.gz
RUN curl -L https://osf.io/ev85t/?download=1 > /datacarpentry/.rawdata/SRR2584858_2.fastq.gz
RUN curl -L https://osf.io/jqdxf/?download=1 > /datacarpentry/.rawdata/SRR2584859_1.fastq.gz
RUN curl -L https://osf.io/5y9nu/?download=1 > /datacarpentry/.rawdata/SRR2584859_2.fastq.gz
RUN curl -L https://osf.io/eaynk/?download=1 > /datacarpentry/.rawdata/SRR2584860_1.fastq.gz
RUN curl -L https://osf.io/qtng9/?download=1 > /datacarpentry/.rawdata/SRR2584860_2.fastq.gz
# Make the raw data read-only!!!
RUN chmod 444 /datacarpentry/.rawdata/SRR*.fastq.gz

# Register and execute the `dcsetup` command for populating the
# `/datacarpentry/data/` working directory.
RUN cat /datacarpentry/.bashrc >> ~/.bashrc
RUN bash -c "source /datacarpentry/.bashrc && dcsetup"

CMD bash
6 changes: 6 additions & 0 deletions bashrc
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dcsetup()
{
rm -rf /datacarpentry/data/
mkdir -p /datacarpentry/data/
ln -s /datacarpentry/.rawdata/SRR*.fastq.gz /datacarpentry/data/.
}