Initial test of diamond 2.2.1. Issues with downloading test file. Add…

build-files/diamond/2.2.1/Dockerfile

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+FROM ubuntu:noble AS app
+
+ARG DIAMOND_VER="2.2.1"
+
+LABEL base.image="ubuntu:noble"
+LABEL dockerfile.version="1"
+LABEL software="DIAMOND"
+LABEL software.version="${DIAMOND_VER}"
+LABEL description="Accelerated BLAST compatible local sequence aligner."
+LABEL website="https://github.com/bbuchfink/diamond"
+LABEL license="https://github.com/bbuchfink/diamond/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluhan.incekara@ct.gov"
+LABEL maintainer2="Raheel Ahmed"
+LABEL maintainer2.email="raheelsyedahmed@gmail.com"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget -q https://github.com/bbuchfink/diamond/releases/download/v${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 apt-get update && apt-get install -y --no-install-recommends \
+    curl && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN diamond test
+
+# Currently running into an issue with this URL, where a bot catcher page (Anubis Web Firewall Utility) prevents access before redirecting to the file directory.
+# Alternatives I've tried that have not succeeded:
+#   wget https://scop.berkeley.edu/downloads/scopeseq-2.07/astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa
+#   curl -L -A 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/120.0.0.0 Safari/537.36' 'https://scop.berkeley.edu/downloads/scopeseq-2.07/astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa' -o 'astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa'
+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 &&\
+    cat 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/2.2.1/README.md

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+# 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
+```