adding datasets version 16.35.0 (#1103)

* adding datasets version 16.35.0

* Update README.md

Fix merge issues

---------

Co-authored-by: Kutluhan Incekara <[email protected]>

README.md

@@ -221,7 +221,7 @@ 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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | <ul><li>0.11.0 (Mykrobe) & 1.9.1 (Genotyphi) </li><li>0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping) </li><li>0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) </li><li>[0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](mykrobe/0.12.2/)</li><li>[0.13.0](./mykrobe/0.13.0)</li></ul> | https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/typhoidgenomics/genotyphi <br/> https://github.com/katholt/sonneityping |
 | [NanoPlot](https://hub.docker.com/r/staphb/nanoplot) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/nanoplot)](https://hub.docker.com/r/staphb/nanoplot) | <ul><li>[1.27.0](./nanoplot/1.27.0/)</li><li>[1.29.0](./nanoplot/1.29.0/)</li><li>[1.30.1](./nanoplot/1.30.1/)</li><li>[1.32.0](./nanoplot/1.32.0/)</li><li>[1.33.0](./nanoplot/1.33.0/)</li><li>[1.40.0](./nanoplot/1.40.0/)</li><li>[1.41.6](./nanoplot/1.41.6/)</li><li>[1.42.0](./nanoplot/1.42.0/)</li></ul> | https://github.com/wdecoster/NanoPlot |
 | [ngmaster](https://hub.docker.com/r/staphb/ngmaster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ngmaster)](https://hub.docker.com/r/staphb/ngmaster) | <ul><li>0.5.8</li><li>1.0.0</li></ul> | https://github.com/MDU-PHL/ngmaster |
-| [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) | <details><summary> Click to see all datasets versions </summary> **datasets versions** <ul><li>[13.31.0](./ncbi-datasets/13.31.0/)</li><li>[13.35.0](./ncbi-datasets/13.35.0/)</li><li>[13.43.2](./ncbi-datasets/13.43.2/)</li><li>[14.0.0](./ncbi-datasets/14.0.0/)</li><li>[14.3.0](./ncbi-datasets/14.3.0/)</li><li>[14.7.0](./ncbi-datasets/14.7.0/)</li><li>[14.13.2](./ncbi-datasets/14.13.2/)</li><li>[14.20.0](./ncbi-datasets/14.20.0/)</li><li>[14.27.0](ncbi-datasets/14.27.0/)</li><li>[15.1.0](ncbi-datasets/15.1.0/)</li><li>[15.2.0](ncbi-datasets/15.2.0/)</li><li>[15.11.0](ncbi-datasets/15.11.0/)</li><li>[15.27.1](ncbi-datasets/15.27.1/)</li><li>[15.31.0](ncbi-datasets/15.31.1/)</li><li>[16.2.0](ncbi-datasets/16.2.0/)</li><li>[16.8.1](./ncbi-datasets/16.8.1/)</li><li>[16.10.3](./ncbi-datasets/16.10.3/)</li><li>[16.15.0](./ncbi-datasets/16.15.0/)</li><li>[16.22.1](./ncbi-datasets/16.22.1/)</li><li>[16.30.0](./ncbi-datasets/16.30.0/)</li></ul> | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets) <br/>[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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) | <details><summary> Click to see all datasets versions </summary> **datasets versions** <ul><li>[13.31.0](./ncbi-datasets/13.31.0/)</li><li>[13.35.0](./ncbi-datasets/13.35.0/)</li><li>[13.43.2](./ncbi-datasets/13.43.2/)</li><li>[14.0.0](./ncbi-datasets/14.0.0/)</li><li>[14.3.0](./ncbi-datasets/14.3.0/)</li><li>[14.7.0](./ncbi-datasets/14.7.0/)</li><li>[14.13.2](./ncbi-datasets/14.13.2/)</li><li>[14.20.0](./ncbi-datasets/14.20.0/)</li><li>[14.27.0](ncbi-datasets/14.27.0/)</li><li>[15.1.0](ncbi-datasets/15.1.0/)</li><li>[15.2.0](ncbi-datasets/15.2.0/)</li><li>[15.11.0](ncbi-datasets/15.11.0/)</li><li>[15.27.1](ncbi-datasets/15.27.1/)</li><li>[15.31.0](ncbi-datasets/15.31.1/)</li><li>[16.2.0](ncbi-datasets/16.2.0/)</li><li>[16.8.1](./ncbi-datasets/16.8.1/)</li><li>[16.10.3](./ncbi-datasets/16.10.3/)</li><li>[16.15.0](./ncbi-datasets/16.15.0/)</li><li>[16.22.1](./ncbi-datasets/16.22.1/)</li><li>[16.30.0](./ncbi-datasets/16.30.0/)</li><li>[16.35.0](ncbi-datasets/16.35.0/)</li></ul> | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets) <br/>[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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion** <details><summary> Click to see AMRFinderplus v3.11.4 and older versions! </summary> <ul><li>3.1.1b</li><li>3.8.4</li><li>3.8.28</li><li>3.9.3</li><li>3.9.8</li><li>3.10.1</li><li>3.10.5</li><li>3.10.16</li><li>3.10.20</li><li>3.10.24</li><li>3.10.30</li><li>3.10.36</li><li>3.10.42</li><li>3.11.2 & 2022-12-19.1</li><li>[3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)</li><li>[3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)</li></ul> </details> <ul><li>[3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)</li><li>[3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)</li><li>[3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)</li><li>[3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)</li><li>[3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)</li><li>[3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)</li><li>[3.11.26 & 2023-11-15.1](ncbi-amrfinderplus/3.11.26-2023-11-15.1/)</li><li>[3.12.8 & 2024-01-31.1](ncbi-amrfinderplus/3.12.8-2024-01-31.1/)</li><li>[3.12.8 & 2024-05-02.2](./ncbi-amrfinderplus/3.12.8-2024-05-02.2/)</li><li>[3.12.8 & 2024-07-22.1](./ncbi-amrfinderplus/3.12.8-2024-07-22.1/)</li><li>[4.0.3 & 2024-10-22.1 (includes stxtyper)](./ncbi-amrfinderplus/4.0.3-2024-10-22.1/)</li></ul> | [https://github.com/ncbi/amr](https://github.com/ncbi/amr) |
 | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) | <ul><li>[1.26.678](./ncbi-table2asn/1.26.678/)</li><li>[1.28.943](./ncbi-table2asn/1.28.943/)</li><li>[1.28.1021](./ncbi-table2asn/1021/)</li></ul> | [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/) <br/>[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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) | <ul><li>[0.2.3](ontime/0.2.3/)</li><li>[0.3.1](ontime/0.3.1/)</li></ul> | https://github.com/mbhall88/ontime |

ncbi-datasets/16.35.0/Dockerfile

@@ -0,0 +1,46 @@
+FROM ubuntu:jammy as app
+
+ARG DATASETS_VER="16.35.0"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="NCBI's datasets and dataformat"
+LABEL software.version="${DATASETS_VER}"
+LABEL description="Downloads biological sequence data from NCBI"
+LABEL website="https://www.ncbi.nlm.nih.gov/datasets/docs/v1/"
+LABEL license="https://github.com/ncbi/datasets/blob/master/pkgs/ncbi-datasets-cli/LICENSE.md"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+# unzip isn't needed for datasets/dataformat, but it is often used after downloading files with datasets
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ wget \
+ ca-certificates \
+ unzip && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /usr/local/bin
+
+# install ncbi datasets tool (pre-compiled binary)
+RUN wget https://github.com/ncbi/datasets/releases/download/v${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 <subcommand> --help, but just typing in 'datasets' should bring up a help menu
+CMD [ "datasets" ]
+
+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

ncbi-datasets/16.35.0/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
+```