adding diamond version 2.1.10 (#1089)

README.md

@@ -149,7 +149,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [colorid](https://hub.docker.com/r/staphb/colorid) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/colorid)](https://hub.docker.com/r/staphb/colorid) | <ul><li>0.1.4.3</li></ul> | https://github.com/hcdenbakker/colorid |
 | [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) | <ul><li>1.0.0</li></ul> | 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) | <ul><li>0.6.2</li><li>0.6.3</li><li>0.7.2</li></ul> | https://github.com/CDCgov/datasets-sars-cov-2 |
-| [diamond](https://github.com/bbuchfink/diamond) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/diamond)](https://hub.docker.com/r/staphb/diamond) | <ul><li>[2.1.9](./diamond/2.1.9)</li></ul> | 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) | <ul><li>[2.1.9](./diamond/2.1.9)</li><li>[2.1.10](./diamond/2.1.10)</li></ul> | https://github.com/bbuchfink/diamond|
 | [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) | <ul><li>[0.1.0](dnaapler/0.1.0/)</li></ul> <ul><li>[0.4.0](dnaapler/0.4.0/)</li><li>[0.5.0](./dnaapler/0.5.0/)</li><li>[0.5.1](./dnaapler/0.5.1/)</li><li>[0.7.0](./dnaapler/0.7.0/)</li><li>[0.8.0](./dnaapler/0.8.0/)</li><li>[0.8.1](./dnaapler/0.8.1/)</li></ul> | https://github.com/gbouras13/dnaapler |
 | [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) | <ul><li>[0.8.0](dorado/0.8.0/)</li></ul> | [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) | <ul><li>[1.0.14](./dragonflye/1.0.14/)</li><li>[1.1.1](./dragonflye/1.1.1/)</li><li>[1.1.2](./dragonflye/1.1.2/)</li><li>[1.2.0](./dragonflye/1.2.0/)</li><li>[1.2.1](./dragonflye/1.2.1/)</li></ul> | https://github.com/rpetit3/dragonflye |

diamond/2.1.10/Dockerfile

@@ -0,0 +1,38 @@
+FROM ubuntu:jammy as app
+
+ARG DIAMOND_VER="2.1.10"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="DIAMOND"
+LABEL software.version="${DIAMOND_VER}"
+LABEL description="Accelerated BLAST compatible local sequence aligner."
+LABEL website="https://github.com/bbuchfink/diamond"
+LABEL license="https://github.com/bbuchfink/diamond/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ncbi-blast+ &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate https://github.com/bbuchfink/diamond/releases/download/v${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 --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

diamond/2.1.10/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:
+- ncbi-blast+ : 2.12.0
+
+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
+```