diff --git a/README.md b/README.md index ef5332d0d..d26636df5 100644 --- a/README.md +++ b/README.md @@ -288,7 +288,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Trycycler](https://hub.docker.com/r/staphb/trycycler/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/trycycler)](https://hub.docker.com/r/staphb/trycycler) | | https://github.com/rrwick/Trycycler | | [Unicycler](https://hub.docker.com/r/staphb/unicycler/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/unicycler)](https://hub.docker.com/r/staphb/unicycler) | | https://github.com/rrwick/Unicycler | | [VADR](https://hub.docker.com/r/staphb/vadr/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/vadr)](https://hub.docker.com/r/staphb/vadr) | | https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr)
https://github.com/ncbi/vadr | -| [Verkko](https://hub.docker.com/r/staphb/verkko/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/verkko)](https://hub.docker.com/r/staphb/verkko) | | https://github.com/marbl/verkko | +| [Verkko](https://hub.docker.com/r/staphb/verkko/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/verkko)](https://hub.docker.com/r/staphb/verkko) | | https://github.com/marbl/verkko | | [VIBRANT](https://hub.docker.com/r/staphb/vibrant/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/vibrant)](https://hub.docker.com/r/staphb/vibrant) | | https://github.com/AnantharamanLab/VIBRANT | | [VIGOR4](https://hub.docker.com/r/staphb/vigor4/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/vigor4)](https://hub.docker.com/r/staphb/vigor4) | | https://github.com/JCVenterInstitute/VIGOR4 | | [VirSorter2](https://hub.docker.com/r/staphb/virsorter2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/virsorter2)](https://hub.docker.com/r/staphb/virsorter2/) | | https://github.com/jiarong/VirSorter2 | diff --git a/verkko/2.1/Dockerfile b/verkko/2.1/Dockerfile new file mode 100644 index 000000000..5f77f5fba --- /dev/null +++ b/verkko/2.1/Dockerfile @@ -0,0 +1,48 @@ +FROM mambaorg/micromamba:1.5.8 as app + +ARG VERKKO_VER="2.1" + +USER root + +WORKDIR / + +LABEL base.image="mambaorg/micromamba:1.5.8" +LABEL dockerfile.version="1" +LABEL software="Verkko" +LABEL software.version="${VERKKO_VER}" +LABEL description="Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads." +LABEL website="https://github.com/marbl/verkko" +LABEL license="https://github.com/marbl/verkko/blob/master/README.licenses" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y \ + procps &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN micromamba install --name base -c conda-forge -c bioconda verkko=${VERKKO_VER} && \ + micromamba clean -afy + +ENV PATH="/opt/conda/bin/:${PATH}" \ + LC_ALL=C.UTF-8 + +CMD [ "verkko", "--help" ] + +WORKDIR /data + +## Test ## +FROM app as test + +RUN verkko --help + +RUN apt-get update && apt-get install --no-install-recommends -y curl + +# test data +RUN curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz -o hifi.fastq.gz &&\ + curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz -o ont.fastq.gz + +# verkko test run +RUN verkko -d asm --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz &&\ + head asm/assembly.hifi-coverage.csv &&\ + head -c 1000 asm/assembly.fasta + diff --git a/verkko/2.1/README.md b/verkko/2.1/README.md new file mode 100644 index 000000000..ee3b2e499 --- /dev/null +++ b/verkko/2.1/README.md @@ -0,0 +1,21 @@ +# Verkko container + +Main tool: [verkko](https://github.com/marbl/verkko) + +Code repository: https://github.com/marbl/verkko + +Basic information on how to use this tool: +- executable: verkko +- help: --help +- version: --version +- description: Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads. + +Full documentation: https://github.com/marbl/verkko + +## Example Usage + +```bash +verkko -d --hifi [--nano ] +``` + + \ No newline at end of file