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# FROM ubuntu:bionic
FROM tomkellygenetics/cellranger_clean:3.0.2.9002
RUN apt-get update \
&& apt-get upgrade -y \
&& apt-get install -y \
git \
git-lfs \
make \
gzip \
pigz \
rename
RUN apt-get install -y \
curl \
zsh \
nano \
&& sh -c "$(curl -fsSL https://raw.github.com/ohmyzsh/ohmyzsh/master/tools/install.sh) --unattended"
RUN apt-get install -y \
python3-pip \
&& python3 -m pip install --upgrade pip setuptools wheel \
&& pip3 install multiqc
RUN git clone https://github.com/linsalrob/fastq-pair.git \
&& cd fastq-pair \
&& mkdir build \
&& cd build \
&& gcc -std=gnu99 ../main.c ../robstr.c ../fastq_pair.c ../is_gzipped.c -o fastq_pair \
&& cp fastq_pair /bin/fastq_pair
# Install STAR aligner
RUN wget https://github.com/alexdobin/STAR/archive/2.5.1b.tar.gz \
&& tar -xf 2.5.1b.tar.gz \
&& rm 2.5.1b.tar.gz \
&& cd STAR-2.5.1b \
&& make \
&& mv bin/Linux_x86_64/STAR* /usr/bin \
&& cd source \
&& make \
&& cd /
RUN chmod -R 777 /cellranger-3.0.2.9001/*
RUN git clone "https://github.com/minoda-lab/universc.git"
RUN cd universc/test/cellranger_reference/cellranger-tiny-ref/ \
&& git lfs pull \
&& rm -rf 3.0.0 1.2.0 \
&& cellranger mkref --genome=3.0.0 --fasta=genome-3.0.0.fa --genes=genes-3.0.0.gtf \
&& cellranger mkref --genome=1.2.0 --fasta=genome-1.2.0.fa --genes=genes-1.2.0.gtf
COPY .version universc/.version
COPY CHANGELOG universc/CHANGELOG
COPY README.Rmd universc/README.Rmd
COPY README.md universc/README.md
COPY README.html universc/README.html
COPY inst/CITATION universc/inst/CITATION
COPY launch_universc.sh universc/launch_universc.sh
COPY sub/FilterSmartSeqReadUMI.pl universc/sub/FilterSmartSeqReadUMI.pl
RUN cd universc \
&& make reference \
&& cd ..
RUN mkdir -p /cellranger-3.0.2.9001/cellranger-tiny-fastq \
&& ln -s /universc/test/shared/cellranger-tiny-fastq/1.2.0 /cellranger-3.0.2.9001/cellranger-tiny-fastq \
&& ln -s /universc/test/shared/cellranger-tiny-fastq/3.0.0 /cellranger-3.0.2.9001/cellranger-tiny-fastq
RUN mkdir -p /cellranger-3.0.2.9001/cellranger-tiny-ref \
&& ln -s /universc/test/cellranger_reference/cellranger-tiny-ref/1.2.0 /cellranger-3.0.2.9001/cellranger-tiny-ref \
&& ln -s /universc/test/cellranger_reference/cellranger-tiny-ref/3.0.0 /cellranger-3.0.2.9001/cellranger-tiny-ref
RUN ln -s /universc/launch_universc.sh /universc/universc
ENV PATH /universc:$PATH
COPY ./launch_universc.sh /universc/launch_universc.sh
RUN ln /universc/launch_universc.sh /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/universc
RUN ln -s /universc/sub /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/sub
RUN ln -s /universc/whitelists /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/whitelists
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8
RUN cp /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/chemistry.py /cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python/cellranger/check.py
RUN chmod -R 777 /cellranger-3.0.2.9001/* /universc/*
RUN chmod a+w /cellranger-3.0.2.9001 /universc