Merge pull request #1570 from cwoodside1278/diamond-2.1.23

Update to Diamond 2.1.23

Author: erinyoung

README.md

@@ -155,7 +155,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [cutshaw-report-env](https://hub.docker.com/r/staphb/cutshaw-report-env) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cutshaw-report-env)](https://hub.docker.com/r/staphb/cutshaw-report-env) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.0](./build-files/cutshaw-report-env/1.0/)</li></ul> </details> | https://github.com/VADGS/CutShaw |
 | [datasets-sars-cov-2](https://github.com/CDCgov/datasets-sars-cov-2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) | <details><summary>Click to see all versions</summary> <ul><li>[0.6.2](./build-files/datasets-sars-cov-2/0.6.2/)</li><li>[0.6.3](./build-files/datasets-sars-cov-2/0.6.3/)</li><li>[0.7.2](./build-files/datasets-sars-cov-2/)</li></ul> </details> | https://github.com/CDCgov/datasets-sars-cov-2 |
 | [dnaapler](https://hub.docker.com/r/staphb/dnaapler) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dnaapler)](https://hub.docker.com/r/staphb/dnaapler) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.0](./build-files/dnaapler/0.1.0/)</li></ul> <ul><li>[0.4.0](./build-files/dnaapler/0.4.0/)</li><li>[0.5.0](./build-files/dnaapler/0.5.0/)</li><li>[0.5.1](./build-files/dnaapler/0.5.1/)</li><li>[0.7.0](./build-files/dnaapler/0.7.0/)</li><li>[0.8.0](./build-files/dnaapler/0.8.0/)</li><li>[1.0.1](./build-files/dnaapler/1.0.1/)</li><li>[1.1.0](./build-files/dnaapler/1.1.0/)</li><li>[1.2.0](./build-files/dnaapler/1.2.0/)</li><li>[1.3.0](./build-files/dnaapler/1.3.0/)</li></ul> </details> | https://github.com/gbouras13/dnaapler |
-| [diamond](https://github.com/bbuchfink/diamond) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/diamond)](https://hub.docker.com/r/staphb/diamond) | <details><summary>Click to see all versions</summary> <ul><li>[2.1.9](./build-files/diamond/2.1.9)</li><li>[2.1.10](./build-files/diamond/2.1.10)</li><li>[2.1.11](./build-files/diamond/2.1.11)</li><li>[2.1.12](./build-files/diamond/2.1.12)</li><li>[2.1.13](./build-files/diamond/2.1.13)</li><li>[2.1.16](./build-files/diamond/2.1.16)</li><li>[2.1.22](./build-files/diamond/2.1.22)</li></ul> </details> | https://github.com/bbuchfink/diamond|
+| [diamond](https://github.com/bbuchfink/diamond) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/diamond)](https://hub.docker.com/r/staphb/diamond) | <details><summary>Click to see all versions</summary> <ul><li>[2.1.9](./build-files/diamond/2.1.9)</li><li>[2.1.10](./build-files/diamond/2.1.10)</li><li>[2.1.11](./build-files/diamond/2.1.11)</li><li>[2.1.12](./build-files/diamond/2.1.12)</li><li>[2.1.13](./build-files/diamond/2.1.13)</li><li>[2.1.16](./build-files/diamond/2.1.16)</li><li>[2.1.22](./build-files/diamond/2.1.22)</li><li>[2.1.23](./build-files/diamond/2.1.23)</li></ul> </details> | https://github.com/bbuchfink/diamond|
 | [dorado](https://hub.docker.com/r/staphb/dorado) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dorado)](https://hub.docker.com/r/staphb/dorado) | <details><summary>Click to see all versions</summary> <ul><li>[0.8.0](./build-files/dorado/0.8.0/)</li><li>[0.8.3](./build-files/dorado/0.8.3/)</li><li>[0.9.0](./build-files/dorado/0.9.0-cuda12.2.0/)</li><li>[0.9.0-cuda12.2.0-no_model](./build-files/dorado/0.9.0-cuda12.2.0-no_model/)</li><li>[1.1.0-cuda12.2.0](./build-files/dorado/1.1.0-cuda12.2.0/)</li><li>[1.1.0-cuda12.2.0-no_model](./build-files/dorado/1.1.0-cuda12.2.0-no_model/)</li></ul></ul> </details> | [https://github.com/nanoporetech/dorado](https://github.com/nanoporetech/dorado) |
 | [dragonflye](https://hub.docker.com/r/staphb/dragonflye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dragonflye)](https://hub.docker.com/r/staphb/dragonflye) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.14](./build-files/dragonflye/1.0.14/)</li><li>[1.1.1](./build-files/dragonflye/1.1.1/)</li><li>[1.1.2](./build-files/dragonflye/1.1.2/)</li><li>[1.2.0](./build-files/dragonflye/1.2.0/)</li><li>[1.2.1](./build-files/dragonflye/1.2.1/)</li></ul> </details> | https://github.com/rpetit3/dragonflye |
 | [Dr. PRG ](https://hub.docker.com/r/staphb/drprg) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/drprg)](https://hub.docker.com/r/staphb/drprg) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.1](./build-files/drprg/0.1.1/)</li></ul> </details> | https://mbh.sh/drprg/ |

build-files/diamond/2.1.23/Dockerfile

@@ -0,0 +1,37 @@
+FROM ubuntu:noble AS app
+
+ARG DIAMOND_VER="2.1.23"
+
+LABEL base.image="ubuntu:noble"
+LABEL dockerfile.version="1"
+LABEL software="DIAMOND"
+LABEL software.version="${DIAMOND_VER}"
+LABEL description="Accelerated BLAST compatible local sequence aligner."
+LABEL website="https://github.com/bbuchfink/diamond"
+LABEL license="https://github.com/bbuchfink/diamond/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluhan.incekara@ct.gov"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --quiet --no-check-certificate https://github.com/bbuchfink/diamond/releases/download/v${DIAMOND_VER}/diamond-linux64.tar.gz &&\
+    tar -C /usr/local/bin -xvf diamond-linux64.tar.gz && \
+    rm diamond-linux64.tar.gz
+
+ENV LC_ALL=C
+
+CMD [ "diamond", "help" ]
+
+WORKDIR /data
+
+## Test ##
+FROM app AS test
+
+RUN diamond test
+
+RUN wget --quiet --no-check-certificate https://scop.berkeley.edu/downloads/scopeseq-2.07/astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa &&\
+    diamond makedb --in astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa -d astral40 &&\
+    diamond blastp -q astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa -d astral40 -o out.tsv --very-sensitive &&\
+    head out.tsv

build-files/diamond/2.1.23/README.md

@@ -0,0 +1,32 @@
+# diamond container
+
+Main tool: [diamond](https://github.com/bbuchfink/diamond)
+  
+Code repository: https://github.com/bbuchfink/diamond
+
+Additional tools:
+- none
+
+Basic information on how to use this tool:
+- executable: `diamond`
+- help: `help`
+- version: `version`
+- description: DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:
+
+  - Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST.
+  - Protein clustering of up to tens of billions of proteins
+  - Frameshift alignments for long read analysis.
+  - Low resource requirements and suitable for running on standard desktops or laptops.
+  - Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.
+
+Full documentation: https://github.com/bbuchfink/diamond/wiki
+
+## Example Usage
+
+```bash
+# Protein alignment
+diamond makedb --in proteins.fa -d db
+diamond blastp -q query.fa -d db -o out.tsv --very-sensitive
+# Protein clustering
+diamond cluster -d proteins.fa -o clusters.tsv --approx-id 40 -M 12G --header
+```