adds quast 5.3.0-slim

README.md

@@ -255,7 +255,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | <ul><li>0.2.2</li><li>0.3.2</li><li>[0.4.2](pygenomeviz/0.4.2/)</li><li>[0.4.3](pygenomeviz/0.4.3/)</li><li>[0.4.4](pygenomeviz/0.4.4/)</li><li>[1.1.0](pygenomeviz/1.1.0/)</li></ul> | https://github.com/moshi4/pyGenomeViz |
 | [pyMLST](https://hub.docker.com/r/staphb/pymlst/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pymlst)](https://hub.docker.com/r/staphb/pymlst) | <ul><li>[2.1.5](./pymlst/2.1.5/)</li><li>[2.1.6](./pymlst/2.1.6/)</li></ul> | https://github.com/bvalot/pyMLST |
 | [pypolca](https://hub.docker.com/r/staphb/pypolca/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pypolca)](https://hub.docker.com/r/staphb/pypolca) | <ul><li>[0.3.1](./pypolca/0.3.1/)</li></ul> | https://github.com/gbouras13/pypolca |
-| [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 |
+| [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><li>[5.3.0](./quast/5.3.0)</li><li>[5.3.0-slim](./quast/5.3.0-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><li>[2.1.0](./rasusa/2.1.0/)</li></ul> | https://github.com/mbhall88/rasusa |

quast/5.3.0-slim/Dockerfile

@@ -0,0 +1,45 @@
+FROM ubuntu:jammy as app
+
+ARG QUAST_VER="5.3.0"
+ARG MINIMAP2_VER="2.28"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="QUAST"
+LABEL software.version=${QUAST_VER}
+LABEL description="Genome assembly evaluation tool"
+LABEL website="https://github.com/ablab/quast"
+LABEL license="https://github.com/ablab/quast/blob/master/LICENSE.txt"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    bzip2 \
+    python-is-python3 \
+    locales &&\
+    locale-gen en_US.UTF-8 &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 &&\
+    tar --no-same-owner -jxvf minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 && rm minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 &&\
+    wget --no-check-certificate https://github.com/ablab/quast/releases/download/quast_${QUAST_VER}/quast-${QUAST_VER}.tar.gz &&\
+    tar -xvf quast-${QUAST_VER}.tar.gz && rm quast-${QUAST_VER}.tar.gz
+
+ENV PATH=$PATH:/quast-${QUAST_VER}:/minimap2-${MINIMAP2_VER}_x64-linux/ \
+    LC_ALL=C
+
+CMD quast.py --help && quast-lg.py --help && metaquast.py --help
+
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+ARG QUAST_VER
+ARG DPATH="/quast-${QUAST_VER}/test_data"
+
+# test quast
+RUN quast.py ${DPATH}/contigs_1.fasta ${DPATH}/contigs_2.fasta -r ${DPATH}/reference.fasta.gz -o quast_out
+# test metaquast
+RUN metaquast.py ${DPATH}/meta_contigs_1.fasta ${DPATH}/meta_contigs_2.fasta -r ${DPATH}/meta_ref_1.fasta,${DPATH}/meta_ref_2.fasta,${DPATH}/meta_ref_3.fasta -o metaquast_out

quast/5.3.0-slim/README.md

@@ -0,0 +1,31 @@
+# QUAST slim container
+
+Main tool: [QUAST](https://github.com/ablab/quast)
+
+Code repository: https://github.com/ablab/quast
+
+Additional tools:
+- minimap2 2.28-r1209
+
+Basic information on how to use this tool:
+- executable: quast.py
+- help: --help
+- version: --version
+- description: Genome assembly evaluation tool
+
+Additional information:
+
+This image provides minimal requirements of QUAST. Some of the functions may not work. Please use **staphb/quast:5.3.0** for the full functionality of the program.
+
+Full documentation: https://quast.sourceforge.net/docs/manual.html
+
+## Example Usage
+
+```bash
+# basic statistics without reference
+quast.py contigs.fasta
+# genome evaluation with reference
+quast.py contigs.fasta -r reference.fasta.gz
+# metagenomic assemblies
+metaquast.py contigs_1 contigs_2 ... -r reference_1,reference_2,reference_3,...
+```