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Dockerfile
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FROM python:3.11
MAINTAINER Kez Cleal [email protected]
USER root
ENV VIRTUAL_ENV=/opt/venv
RUN python3 -m venv $VIRTUAL_ENV
ENV PATH="$VIRTUAL_ENV/bin:$PATH"
RUN pip install dysgu==1.6.2 && \
wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 && \
tar -xvf samtools-1.18.tar.bz2 && \
rm samtools-1.18.tar.bz2 && \
mv samtools-1.18 samtools && \
cd samtools && ./configure && \
make && \
make install && \
cd ../ && \
wget https://github.com/samtools/bcftools/releases/download/1.18/bcftools-1.18.tar.bz2 && \
tar -xvf bcftools-1.18.tar.bz2 && \
rm bcftools-1.18.tar.bz2 && \
mv bcftools-1.18 bcftools && \
cd bcftools && \
./configure && \
make && \
make install && \
cd ../
CMD ["/bin/sh"]
# Docker user guide
# -----------------
## Make an 'input_folder', put your bam file and reference genome inside:
# ./input_folder/
# sample.bam
# reference.fasta
# reference.fasta.fai
## Make an 'output_folder'
# mkdir output_folder
## Set up docker
# docker pull kcleal/dysgu
# docker run -it \
# --mount src="${PWD}"/input_folder,target=/input_folder,type=bind \
# --mount src="${PWD}"/output_folder,target=/output_folder,type=bind \
# kcleal/dysgu
# cd input_folder
## Run dysgu:
# dysgu run reference.fasta wd sample.bam > ../output_folder/sample.vcf
# exit