adding rasusa version 2.1.0

README.md

@@ -252,7 +252,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [QUAST](https://hub.docker.com/r/staphb/quast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | <ul><li>5.0.0</li><li>5.0.2</li><li>[5.2.0](./quast/5.2.0)</li><li>[5.2.0-slim](./quast/5.2.0-slim)</li></ul> | https://github.com/ablab/quast |
 | [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | <ul><li>1.0.1</li></ul> | https://github.com/k-florek/QuickSNP |
 | [racon](https://hub.docker.com/r/staphb/racon) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| <ul><li>[1.4.3](./racon/1.4.3/)</li><li>[1.4.20](./racon/1.4.20/)</li><li>[1.5.0](./racon/1.5.0/)</li></ul> | <li> https://github.com/lbcb-sci/racon </li><li> https://github.com/isovic/racon (ARCHIVED)</li> |
-| [rasusa](https://hub.docker.com/r/staphb/rasusa/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | <ul><li>[0.1.0](./rasusa/0.1.0/)</li><li>[0.2.0](./rasusa/0.2.0/)</li><li>[0.3.0](./rasusa/0.3.0/)</li><li>[0.6.0](./rasusa/0.6.0/)</li><li>[0.7.0](./rasusa/0.7.0/)</li><li>[0.8.0](./rasusa/0.8.0/)</li><li>[2.0.0](./rasusa/2.0.0/)</li></ul> | https://github.com/mbhall88/rasusa |
+| [rasusa](https://hub.docker.com/r/staphb/rasusa/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | <ul><li>[0.1.0](./rasusa/0.1.0/)</li><li>[0.2.0](./rasusa/0.2.0/)</li><li>[0.3.0](./rasusa/0.3.0/)</li><li>[0.6.0](./rasusa/0.6.0/)</li><li>[0.7.0](./rasusa/0.7.0/)</li><li>[0.8.0](./rasusa/0.8.0/)</li><li>[2.0.0](./rasusa/2.0.0/)</li><li>[2.1.0](./rasusa/2.1.0/)</li></ul> | https://github.com/mbhall88/rasusa |
 | [raven](https://hub.docker.com/r/staphb/raven/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | <ul><li>1.5.1</li><li>1.8.1</li><li>[1.8.3](./raven/1.8.3)</li></ul> | https://github.com/lbcb-sci/raven |
 | [RAxML](https://hub.docker.com/r/staphb/raxml/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml)](https://hub.docker.com/r/staphb/raxml) | <ul><li>8.2.12</li><li>[8.2.13](./raxml/8.2.13/)</li></ul> | https://github.com/stamatak/standard-RAxML |
 | [RAxML-NG](https://hub.docker.com/r/staphb/raxml-ng/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml-ng)](https://hub.docker.com/r/staphb/raxml-ng) | <ul><li>[1.2.2](./raxml-ng/1.2.2/)</li></ul> | https://github.com/amkozlov/raxml-ng |

rasusa/2.1.0/Dockerfile

@@ -0,0 +1,54 @@
+FROM ubuntu:jammy as app
+
+ARG RASUSA_VER="2.1.0"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="rasusa"
+LABEL software.version="${RASUSA_VER}"
+LABEL description="Randomly subsample sequencing reads to a specified coverage."
+LABEL website="https://github.com/mbhall88/rasusa"
+LABEL license="https://github.com/mbhall88/rasusa/blob/master/LICENSE"
+LABEL maintainer="Jake Garfin"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="[email protected]"
+LABEL maintainer3="Erin Young"
+LABEL maintainer3.email="[email protected]"
+
+# install wget and cleanup apt garbage
+RUN apt-get update && apt-get -y install --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && \
+    rm -rf /var/lib/apt/lists/*
+
+# install rasusa
+RUN wget -q https://github.com/mbhall88/rasusa/releases/download/${RASUSA_VER}/rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu.tar.gz && \
+    tar -xvf rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu.tar.gz && \
+    rm -rf rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu.tar.gz && \
+    mkdir /data
+
+# set PATH and perl locale settings
+ENV PATH="${PATH}:/rasusa-${RASUSA_VER}-x86_64-unknown-linux-gnu/" \
+    LC_ALL=C
+
+WORKDIR /data
+
+CMD rasusa --help
+
+FROM app as test 
+
+# print version and help options
+RUN rasusa --version && rasusa --help
+
+# 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

rasusa/2.1.0/README.md

@@ -0,0 +1,32 @@
+# Rasusa container
+
+Main tool : [Rasusa](https://github.com/mbhall88/rasusa)
+
+Additional tools:
+
+- none
+
+Full documentation: https://github.com/mbhall88/rasusa
+
+Randomly subsample sequencing reads to a specified coverage
+
+## Example Usage
+
+```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
+
+# 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 
+```