namzoo/circleenrich repository overview

FROM condaforge/miniforge3:23.3.1-1

# Install pgltools v2.7.1
RUN pip install PyGLtools
RUN git clone https://github.com/billgreenwald/pgltools.git --branch v2.7.1 && \
	mv pgltools /usr/local/bin/pgltools_files && \
	ln -s /usr/local/bin/pgltools_files/sh/pgltools /usr/local/bin/pgltools
RUN cd /usr/local && ln -s /usr/local/bin/pgltools_files/Python

# For install libssl1.0.0
RUN bash -c 'echo deb http://security.ubuntu.com/ubuntu xenial-security main' >> /etc/apt/sources.list

RUN apt-get update && \
 	DEBIAN_FRONTEND=noninteractive apt-get install --assume-yes \
	gawk \
	vim \
	libssl1.0.0

# Create 'circleEnrich' conda envrionment
RUN git clone https://github.com/henssen-lab/circle-enrich-filter.git && \
	cd circle-enrich-filter && \
	mamba env create -f circleEnrich_env.yml

. /opt/conda/etc/profile.d/conda.sh # singularity
conda activate circleEnrich # docker&singularity

bash /circle-enrich-filter/run_CircleEnrichFilter.sh -i /circle-enrich-filter/example/chp212_2_14508020_18508849.bam -o /output