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FROM foodresearch/bppc
MAINTAINER Mark Fernandes <[email protected]>
ENV SIAB_USER=ngsintro \
SIAB_GROUP=guest \
SIAB_PASSWORD=ngsintro \
SIAB_HOME=/home/$SIAB_USER
ENV DOCS=$SIAB_HOME/docs DATA=$SIAB_HOME/data WORK=$SIAB_HOME/work
USER root
ADD copy_course.sh /scripts/copy_course.sh
RUN chmod +x /scripts/copy_course.sh
# need fastqc, samtools bwa bowtie picard-tools GATK jre wget git
RUN apt-get update && apt-get -y install bowtie bwa curl default-jre fastqc git gzip monit \
picard-tools poppler-utils samtools sudo wget
RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#fix fastqc
RUN mkdir /etc/fastqc && mkdir /etc/fastqc/Configuration
ADD fastqc/* /etc/fastqc/Configuration/
RUN mkdir $DOCS && mkdir $DATA && mkdir $WORK && mkdir /coursehome
#RUN mkdir $DOCS && mkdir $DATA && mkdir $WORK
# Paper & course notes(pdf) use less to read from command-line
# RUN wget -O paper.pdf $DOCS http://f1000research.com/articles/1-2/v2/pdf
# RUN wget -O NGS_tutorial.pdf http://www.walesgenepark.cardiff.ac.uk/wp-content/uploads/2013/04/1.1-Introductory-NGS.pdf
ADD Docs\* $DOCS
ADD Data\* $DATA
ADD GenomeAnalysisTK.jar $SIAB_HOME
ADD Welcome.txt /etc/motd
ADD entrypoint.sh /scripts/entrypoint.sh
ADD launchsiab.sh /scripts/launchsiab.sh
#RUN chmod +x /usr/local/sbin/entrypoint.sh
RUN chmod +x /scripts/entrypoint.sh && chmod +x /scripts/launchsiab.sh
# Description of reads data
# https://figshare.com/collections/Simulated_Illumina_BRCA1_reads_in_FASTQ_format/1641980
# obtain reads that we will be using for analysis exercises
#wget http://files.figshare.com/92198/Brca1Reads_1.1.fastq
#wget http://files.figshare.com/92203/Brca1Reads_1.2.fastq
# Download entire set of reads as zip archive
# https://ndownloader.figshare.com/articles/92338/versions/1
# download read sets from f1000 cloud (S3) volume
# RUN wget -O $DATA/Reads_1.1.fastq https://s3-eu-west-1.amazonaws.com/pstorage-f1000-a46686352/92198/Brca1Reads_1.1.fastq
# RUN wget -O $DATA/Reads_1.2.fastq https://s3-eu-west-1.amazonaws.com/pstorage-f1000-a46686352/92203/Brca1Reads_1.2.fastq
#RUN chown -R $SIAB_USER:$SIAB_GROUP $SIAB_HOME
EXPOSE 22
EXPOSE 4200
VOLUME /coursehome
#USER ngsintro
ENTRYPOINT ["/scripts/launchsiab.sh"]
CMD ["/bin/bash"]