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Copy file name to clipboardExpand all lines: content/news/2026-03-13-galaxy-webhooks-tool-deprecations/index.md
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Galaxy instances accumulate history. That is a strength, but it also creates a familiar problem:
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Some tools remain scientifically valid and still need to run for old workflows to enable
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reproducibility, while newer alternatives are often faster, have better defaults or are easier to
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use. Removing the older tool outright risks breaking reproducibility. Leaving it untouched means
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use. Outright removing the older tool risks breaking reproducibility. Leaving it untouched means
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users keep selecting them out of habit.
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One practical answer is a soft deprecation layer in the Galaxy tool form itself.
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Galaxy already supports site-specific UI extensions through [webhooks](https://docs.galaxyproject.org/en/master/admin/webhooks.html). The same pattern can be used to add a contextual information to
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specific tools. When a user opens an older (still functional tool) Galaxy can display a short
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Galaxy already supports site-specific UI extensions through [webhooks](https://docs.galaxyproject.org/en/master/admin/webhooks.html). The same pattern can be used to add contextual information to
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specific tools. When a user opens an older (still functional) tool, Galaxy can display a short
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notice explaining that the tool is retained for compatibility, why it is no longer the preferred
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choice, and which replacement should be used instead.
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choice, and which replacement tool should be used instead.
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We want to: preserve execution, but improve defaults.
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The `FastQC` to `Falco` transition on the European Galaxy server is a good example. `FastQC` has
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The `FastQC` to `Falco` transition on the European Galaxy server is a good example. `FastQC`is a quality control tool for high-throughput sequence data which has
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been executed more than two million times over the years and is still deeply embedded in many
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sequencing workflows. But `Falco`, published in 2021 as a reimplementation of `FastQC`, is roughly
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three times more efficient. When `Falco` first appeared on the European Galaxy server in June 2024,
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