refactor Docker build to avoid reinstalling STAR, MultiQC, and fastq-pair (3ea1dfea) · Commits · github_fork / Universc

Dockerfile

+23 −29

Original line number	Diff line number	Diff line
		@@ -17,6 +17,29 @@ RUN apt-get install -y \
		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 git clone "https://github.com/TomKellyGenetics/universc.git"

		RUN cd universc/test/cellranger_reference/cellranger-tiny-ref/ \
		@@ -53,35 +76,6 @@ RUN ln -s /universc/launch_universc.sh /cellranger-3.0.2.9001/cellranger-cs/3.0.
		ENV LC_ALL C.UTF-8
		ENV LANG C.UTF-8

		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 wget https://sourceforge.net/projects/bbmap/files/latest/download ; mv download BBMap_38.87.tar.gz \
		# && tar -xvzf BBMap_38.87.tar.gz

		# ENV PATH bbmap:$PATH
		# ENV PATH bbmap:$PATH

		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 +rw /cellranger-3.0.2.9001/*

Admin message