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adding rasusa version 2.1.0 #1067
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erinyoung
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FROM ubuntu:jammy as app | ||
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ARG RASUSA_VER="2.1.0" | ||
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LABEL base.image="ubuntu:jammy" | ||
LABEL dockerfile.version="1" | ||
LABEL software="rasusa" | ||
LABEL software.version="${RASUSA_VER}" | ||
LABEL description="Randomly subsample sequencing reads to a specified coverage." | ||
LABEL website="https://github.com/mbhall88/rasusa" | ||
LABEL license="https://github.com/mbhall88/rasusa/blob/master/LICENSE" | ||
LABEL maintainer="Jake Garfin" | ||
LABEL maintainer.email="[email protected]" | ||
LABEL maintainer2="Curtis Kapsak" | ||
LABEL maintainer2.email="[email protected]" | ||
LABEL maintainer3="Erin Young" | ||
LABEL maintainer3.email="[email protected]" | ||
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# install wget and cleanup apt garbage | ||
RUN apt-get update && apt-get -y install --no-install-recommends \ | ||
wget \ | ||
ca-certificates \ | ||
procps && \ | ||
apt-get autoclean && \ | ||
rm -rf /var/lib/apt/lists/* | ||
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# install rasusa | ||
RUN wget -q https://github.com/mbhall88/rasusa/releases/download/${RASUSA_VER}/rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ | ||
tar -xvf rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ | ||
rm -rf rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl.tar.gz && \ | ||
mkdir /data | ||
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# set PATH and perl locale settings | ||
ENV PATH="${PATH}:/rasusa-${RASUSA_VER}-x86_64-unknown-linux-musl/" \ | ||
LC_ALL=C | ||
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WORKDIR /data | ||
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CMD rasusa --help | ||
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FROM app as test | ||
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# print version and help options | ||
RUN rasusa --version && rasusa --help | ||
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# cannot run rust-based test, since rust isn't installed, but just testing basic command on SC2 reads in our repo | ||
# inputs FASTQs each have 80867 reads | ||
# output FASTQs should have 40434 reads in each (about 1/2 of input) | ||
# -s 1 is for setting a specific seed | ||
# -O is for gzip compression on output FASTQs | ||
RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \ | ||
wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \ | ||
rasusa reads --num 40434 -s 1 -O g -o SRR13957123_downsampled_1.fastq.gz -o SRR13957123_downsampled_2.fastq.gz SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz && \ | ||
ls -lh |
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# Rasusa container | ||
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Main tool : [Rasusa](https://github.com/mbhall88/rasusa) | ||
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Additional tools: | ||
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- none | ||
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Full documentation: https://github.com/mbhall88/rasusa | ||
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Randomly subsample sequencing reads to a specified coverage | ||
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## Example Usage | ||
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```bash | ||
# sars-cov-2 example, paired-end illumina | ||
rasusa reads \ | ||
-n 40434 \ # downsample to specific number of reads per FASTQ file | ||
-s 1 \ # set seed | ||
-O g \ # set output file compression format as gzip | ||
-o SRR13957123_downsampled_1.fastq.gz -o SRR13957123_downsampled_2.fastq.gz \ | ||
SRR13957123_1.fastq.gz SRR13957123_2.fastq.gz | ||
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# Salmonella enterica example, paired-end illumina | ||
rasusa reads \ | ||
--coverage 100 \ # use 100X coverage for downsampling | ||
--genome-size 5M \ # downsample to specific coverage based on genome size (5 million bases) | ||
-s 1 \ # set seed | ||
-O g \ # set output file compression format as gzip | ||
-o SRR10992628_downsampled_1.fastq.gz -o SRR10992628_downsampled_2.fastq.gz \ | ||
SRR10992628_1.fastq.gz SRR10992628_2.fastq.gz | ||
``` |
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Is there any specific reason for using the musl instead of the gnu version? Musl usually tends to be slower. I think gnu may be better since the base image is ubuntu.
Also, rasusa is a single binary that can be extracted directly into /usr/local/bin
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It looks like the gnu version has been available since version 0.7.1, and I just never noticed. I'd call this a legacy issue that I can resolve.