thomasrauter/pbsim3 repository overview

Docker image for PBSIM3, a simulator for all types of Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long reads (https://github.com/yukiteruono/pbsim3/tree/master⁠).

All input files can be mounted to the dir /pbsim3/input_files, and all output is stored in the dir /pbsim3/output_files inside the container (to get the output files out of the container, use docker cp pbsim3:"/pbsim3/output_files" "$(pwd)")

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⁠Example run

docker run --name pbsim3
-v "$(pwd)/myfasta.fasta":/pbsim3/input_files/myfasta.fasta
thomasrauter/pbsim3:1.0
pbsim --strategy wgs
--method qshmm
--qshmm data/QSHMM-RSII.model
--depth 20
--genome input_files/myfasta.fasta

docker cp pbsim3:"/pbsim3/output_files" "$(pwd)"

docker rm pbsim3

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⁠Dockerfile

FROM debian:buster

RUN apt-get update && apt-get install -y
build-essential
zlib1g-dev
libboost-all-dev
git
autoconf
automake
&& rm -rf /var/lib/apt/lists/*

RUN git clone https://github.com/yukiteruono/pbsim3.git⁠

WORKDIR /pbsim3

RUN mkdir -p /pbsim3/input_files

RUN mkdir -p /pbsim3/output_files

RUN ./configure &&
make &&
make install

ENV PATH "/pbsim3/src:${PATH}"

COPY entrypoint.sh /pbsim3/entrypoint.sh

RUN chmod +x /pbsim3/entrypoint.sh

ENTRYPOINT ["/pbsim3/entrypoint.sh"]

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⁠entrypoint.sh

#!/bin/bash pbsim "$@"

files=$(ls -1 | grep -E '.fastq$|.ref$|.maf$|.sam$')

for file in $files; do mv "$file" output_files/ done