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Initial test of diamond 2.2.1. Issues with downloading test file. Add…#1704

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Initial test of diamond 2.2.1. Issues with downloading test file. Add…#1704
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@RaheelSyedAhmed RaheelSyedAhmed commented Jun 10, 2026

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…itional issue with now deprecated command diamond test.

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
    • [] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

This PR is currently a draft PR to assess actions needed for an issue in installing diamond version 2.2.1. An image cannot currently be produced since the test file is unable to be downloaded; the file server for the test file now uses a Web Firewall called Anubis, which sends dummy data back instead of allowing access to the file URL specified. The output of the dummy data is shown below:

Alternative approaches I've attempted include trying to access the file with a user agent and with ca-certificates enabled, but I received the same blocked page data.

<!doctype html><html lang="en"><head><title>Oh noes!</title><link rel="stylesheet" href="/.within.website/x/xess/xess.min.css?cachebuster=1.25.0"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="robots" content="noindex,nofollow"><style>
body,
html {
height: 100%;
display: flex;
justify-content: center;
align-items: center;
margin-left: auto;
margin-right: auto;
}

.centered-div {
text-align: center;
}

#status {
font-variant-numeric: tabular-nums;
}

#progress {
display: none;
width: 90%;
width: min(20rem, 90%);
height: 2rem;
border-radius: 1rem;
overflow: hidden;
margin: 1rem 0 2rem;
outline-offset: 2px;
outline: #b16286 solid 4px;
}

.bar-inner {
background-color: #b16286;
height: 100%;
width: 0;
transition: width 0.25s ease-in;
}
</style><script id="anubis_version" type="application/json">"1.25.0"
</script><script id="anubis_challenge" type="application/json">null
</script><script id="anubis_base_prefix" type="application/json">""
</script><script id="anubis_public_url" type="application/json">""
</script></head><body id="top"><script type="ignore"><a href="/.within.website/x/cmd/anubis/api/honeypot/a95bd6fd-1424-4ea8-a698-5daa774dd1c2/init">Don't click me</a></script><main><h1 id="title" class="centered-div">Oh noes!</h1><div class="centered-div"><img id="image" alt="Sad Anubis" style="width:100%;max-width:256px;" src="/.within.website/x/cmd/anubis/static/img/reject.webp?cacheBuster=1.25.0"><p>Access Denied: error code 3bda83a2c7404d5.</p><p><a href="/">Go home</a> or if you believe you should not be blocked, please contact the webmaster at <a href="mailto:scop@compbio.berkeley.edu">scop@compbio.berkeley.edu</a></p></div><footer><div class="centered-div"><p>Protected by <a href="https://github.com/TecharoHQ/anubis">Anubis</a> From <a href="https://techaro.lol">Techaro</a>. Made with ❤️ in 🇨🇦.</p><p>Mascot design by <a href="https://bsky.app/profile/celphase.bsky.social">CELPHASE</a>.</p><p>This website is running Anubis version <code>1.25.0</code>.</p></div></footer></main></body></html>diamond v2.2.1.181 (C) Max Planck Society for the Advancement of Science, Benjamin J. Buchfink, University of Tuebingen

One other issue is diamond test. The command is now deprecated and shows the following output:

diamond v2.2.1.181 (C) Max Planck Society for the Advancement of Science, Benjamin J. Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
The test workflow is deprecated. Unit testing is available via CTest. No action was taken.

@RaheelSyedAhmed
Initial test of diamond 2.2.1. Issues with downloading test file. Add…
a25e5b7 
…itional issue with now deprecated command diamond test.
@RaheelSyedAhmed

RaheelSyedAhmed commented Jun 10, 2026

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@erinyoung I hope this helps in getting a clearer picture of the issues so far. Let me know if there's any other output data or tests you want me to run.

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