From 041e763160e968fffc7070af91e9663a8d9d6007 Mon Sep 17 00:00:00 2001 From: Young Date: Mon, 18 Mar 2024 10:34:27 -0600 Subject: [PATCH] adding ncbi datasets version 16.8.1 (#919) --- README.md | 2 +- ncbi-datasets/16.8.1/Dockerfile | 47 +++++++++++++++++++++++++++++++++ ncbi-datasets/16.8.1/README.md | 20 ++++++++++++++ 3 files changed, 68 insertions(+), 1 deletion(-) create mode 100644 ncbi-datasets/16.8.1/Dockerfile create mode 100644 ncbi-datasets/16.8.1/README.md diff --git a/README.md b/README.md index e881cf123..c15d583ea 100644 --- a/README.md +++ b/README.md @@ -205,7 +205,7 @@ To learn more about the docker pull rate limits and the open source software pro | [Mykrobe + Genotyphi + sonneityping](https://hub.docker.com/r/staphb/mykrobe)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | | https://github.com/Mykrobe-tools/mykrobe
https://github.com/typhoidgenomics/genotyphi
https://github.com/katholt/sonneityping | | [NanoPlot](https://hub.docker.com/r/staphb/nanoplot)
[![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | | https://github.com/wdecoster/NanoPlot | | [ngmaster](https://hub.docker.com/r/staphb/ngmaster)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | | https://github.com/MDU-PHL/ngmaster | -| [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) |
Click to see all datasets versions **datasets versions** | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets)
[https://www.ncbi.nlm.nih.gov/datasets/docs/v1/](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/) | +| [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) |
Click to see all datasets versions **datasets versions**
  • [13.31.0](./ncbi-datasets/13.31.0/)
  • [13.35.0](./ncbi-datasets/13.35.0/)
  • [13.43.2](./ncbi-datasets/13.43.2/)
  • [14.0.0](./ncbi-datasets/14.0.0/)
  • [14.3.0](./ncbi-datasets/14.3.0/)
  • [14.7.0](./ncbi-datasets/14.7.0/)
  • [14.13.2](./ncbi-datasets/14.13.2/)
  • [14.20.0](./ncbi-datasets/14.20.0/)
  • [14.27.0](ncbi-datasets/14.27.0/)
  • [15.1.0](ncbi-datasets/15.1.0/)
  • [15.2.0](ncbi-datasets/15.2.0/)
  • [15.11.0](ncbi-datasets/15.11.0/)
  • [15.27.1](ncbi-datasets/15.27.1/)
  • [15.31.0](ncbi-datasets/15.31.1/)
  • [16.2.0](ncbi-datasets/16.2.0/)
    • [16.8.1](./ncbi-datasets/16.8.1/)
| [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets)
[https://www.ncbi.nlm.nih.gov/datasets/docs/v1/](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/) | | [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion**
Click to see AMRFinderplus v3.11.4 and older versions!
  • 3.1.1b
  • 3.8.4
  • 3.8.28
  • 3.9.3
  • 3.9.8
  • 3.10.1
  • 3.10.5
  • 3.10.16
  • 3.10.20
  • 3.10.24
  • 3.10.30
  • 3.10.36
  • 3.10.42
  • 3.11.2 & 2022-12-19.1
  • [3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)
  • [3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)
  • [3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)
  • [3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)
  • [3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)
  • [3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)
  • [3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)
  • [3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)
  • [3.11.26 & 2023-11-15.1](ncbi-amrfinderplus/3.11.26-2023-11-15.1/)
  • [3.12.8 & 2024-01-31.1](ncbi-amrfinderplus/3.12.8-2024-01-31.1/)
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) |
  • 1.26.678
| [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | | [ONTime](https://hub.docker.com/r/staphb/ontime)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) |
  • [0.2.3](ontime/0.2.3/)
| https://github.com/mbhall88/ontime | diff --git a/ncbi-datasets/16.8.1/Dockerfile b/ncbi-datasets/16.8.1/Dockerfile new file mode 100644 index 000000000..c74a87b88 --- /dev/null +++ b/ncbi-datasets/16.8.1/Dockerfile @@ -0,0 +1,47 @@ +FROM ubuntu:jammy as app + +ARG DATASETS_VER="16.8.1" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="NCBI's datasets and dataformat" +LABEL software.version="${DATASETS_VER}" +LABEL description="Downloads biological sequence data from NCBI" +LABEL website="https://github.com/ncbi/datasets" +LABEL documentation="https://www.ncbi.nlm.nih.gov/datasets/docs/v1/" +LABEL license="https://github.com/ncbi/datasets/blob/master/pkgs/ncbi-datasets-cli/LICENSE.md" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +# unzip isn't needed for datasets/dataformat, but it is often used after downloading files with datasets +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + unzip && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +WORKDIR /usr/local/bin + +# install ncbi datasets tool (pre-compiled binary) +RUN wget https://github.com/ncbi/datasets/releases/download/v${DATASETS_VER}/linux-amd64.cli.package.zip && \ + unzip linux-amd64.cli.package.zip && \ + rm linux-amd64.cli.package.zip && \ + chmod +x dataformat datasets + +ENV LC_ALL=C + +WORKDIR /data + +# datasets is generally datasets --help, but just typing in 'datasets' should bring up a help menu +CMD [ "datasets", "--help" ] + +FROM app as test + +RUN dataformat --help && datasets --help + +# stolen from Curtis at https://github.com/StaPH-B/docker-builds/blob/master/pangolin/4.1.2/Dockerfile +RUN datasets download virus genome accession ON924087.1 --filename ON924087.1.zip && \ + unzip ON924087.1.zip && \ + rm ON924087.1.zip && \ + cp ncbi_dataset/data/genomic.fna ON924087.1.fna && \ + wc -c ON924087.1.fna diff --git a/ncbi-datasets/16.8.1/README.md b/ncbi-datasets/16.8.1/README.md new file mode 100644 index 000000000..6474b9282 --- /dev/null +++ b/ncbi-datasets/16.8.1/README.md @@ -0,0 +1,20 @@ +# NCBI datasets and dataformat container + +Main tool : [datasets](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/#use-the-datasets-tool-to-download-biological-data) and [dataformat](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/#use-the-dataformat-tool-to-convert-data-reports-to-other-formats) + +Full documentation: [https://www.ncbi.nlm.nih.gov/datasets/docs/v1/how-tos/](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/how-tos/) + +> Use NCBI Datasets to gather metadata, download data packages, view reports and more + +## Example Usage + +```bash +# will download the fasta for ON924087.1 in a zipped directory +datasets download virus genome accession ON924087.1 --filename ON924087.1.zip + +# unzipping the directory and the fasta file will be located at ncbi_dataset/data/genomic.fna +unzip ON924087.1.zip + +# copying the file into something with a better name +cp ncbi_dataset/data/genomic.fna ncbi_dataset/data/ON924087.1.genomic.fna +```