https://wiki.anunna.wur.nl/index.php?action=history&feed=atom&title=Reproducibility_Guidelines 2026-06-20T00:36:50Z Revision history for this page on the wiki MediaWiki 1.45.3 https://wiki.anunna.wur.nl/index.php?title=Reproducibility_Guidelines&diff=2869&oldid=prev 2026-06-18T14:22:22Z

<p>IA migration §8: new Reproducibility Guidelines (versions/containers/Git/WUR GitLab/workflow engines; absorbs Manual GitLab pointer) (via create-page on MediaWiki MCP Server)</p> <p><b>New page</b></p><div>Reproducible work means that you — or someone else — can run your analysis again later and get the same result. On a shared, evolving cluster this takes a little discipline, but the building blocks are all available on Anunna.<br /> <br /> == Pin your software versions ==<br /> <br /> * Load specific module versions rather than defaults, and record the [[Environment Modules|bucket]] and module versions you used. A job that loads &lt;code&gt;Python/3.11.3&lt;/code&gt; from the &lt;code&gt;2024&lt;/code&gt; bucket will behave the same next year; one that loads whatever happens to be current may not.<br /> * For your own environments, pin versions too — record them in a &lt;code&gt;requirements.txt&lt;/code&gt;, &lt;code&gt;environment.yml&lt;/code&gt;, or equivalent. See [[Installing Personal Software]] and [[Python]].<br /> <br /> == Use containers for full reproducibility ==<br /> <br /> A container captures an entire software stack — operating-system libraries, tools, and dependencies — in a single image that runs the same anywhere. On Anunna, use [[Apptainer]] (formerly Singularity). A container is the strongest guarantee that your environment will not drift over time.<br /> <br /> == Keep your code in version control ==<br /> <br /> Track your scripts and pipelines with [https://git-scm.com/ Git] so you have a history of what changed and can return to any version.<br /> <br /> WUR runs a GitLab instance at [https://git.wur.nl git.wur.nl] where you can host your repositories. Set up SSH keys for it the same way as for any SSH service — see [[SSH Access]] for generating a key pair — and add the public key to your GitLab account.<br /> <br /> == Automate the steps ==<br /> <br /> A [[Workflow Engines (Snakemake, Nextflow)|workflow engine]] records the exact steps, their order, and their dependencies, so the whole pipeline can be rerun from scratch. This is far more reproducible than running commands by hand.<br /> <br /> == See also ==<br /> * [[Apptainer]]<br /> * [[Environment Modules]]<br /> * [[Workflow Engines (Snakemake, Nextflow)]]<br /> * [[Installing Personal Software]]</div>

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