diff --git a/README.md b/README.md index 95b9b54cf..43f6df881 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | | https://github.com/moshi4/pyGenomeViz | | [pyMLST](https://hub.docker.com/r/staphb/pymlst/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pymlst)](https://hub.docker.com/r/staphb/pymlst) | | https://github.com/bvalot/pyMLST | | [pypolca](https://hub.docker.com/r/staphb/pypolca/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pypolca)](https://hub.docker.com/r/staphb/pypolca) | | https://github.com/gbouras13/pypolca | -| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | | https://github.com/ablab/quast | +| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quast)](https://hub.docker.com/r/staphb/quast) | | https://github.com/ablab/quast | | [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | | https://github.com/k-florek/QuickSNP | | [racon](https://hub.docker.com/r/staphb/racon)
[![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| |
  • https://github.com/lbcb-sci/racon
  • https://github.com/isovic/racon (ARCHIVED)
  • | | [rasusa](https://hub.docker.com/r/staphb/rasusa/)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | | https://github.com/mbhall88/rasusa | diff --git a/quast/5.3.0-slim/Dockerfile b/quast/5.3.0-slim/Dockerfile new file mode 100644 index 000000000..547ad84fc --- /dev/null +++ b/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=${QUAST_VER} +LABEL description="Genome assembly evaluation tool" +LABEL website="https://github.com/ablab/quast" +LABEL license="https://github.com/ablab/quast/blob/master/LICENSE.txt" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget \ + bzip2 \ + python-is-python3 \ + locales &&\ + locale-gen en_US.UTF-8 &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget --no-check-certificate https://github.com/lh3/minimap2/releases/download/v${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 diff --git a/quast/5.3.0-slim/README.md b/quast/5.3.0-slim/README.md new file mode 100644 index 000000000..61db315cf --- /dev/null +++ b/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,... +``` \ No newline at end of file