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name: deployment-storage description: "Plan and diagnose Snakemake 9.23.1 software deployment, containers, storage providers, caches, archives, and executor jobscript deployment surfaces." disable-model-invocation: true metadata: disco-role: operating license: MIT

Deployment and Storage

Use this sub-skill when a Snakemake workflow needs reproducible software stacks, external storage, cluster/cloud deployment surfaces, source deployment, caches, or archives.

Route here for

• Choosing --software-deployment-method / --sdm, --use-conda, --use-apptainer, or --use-envmodules for a workflow run.
• Writing or diagnosing conda:, global conda:, .pin.txt, .post-deploy.sh, container:, containerized:, and envmodules: directives.
• Planning storage provider usage with --default-storage-provider, --default-storage-prefix, storage: blocks, storage.<tag>(...), local(...), access flags, credentials, or local-copy behavior.
• Handling --shared-fs-usage, non-shared executor storage/cache/source deployment, --jobscript, --jobname, or job properties embedded in jobscripts.
• Creating or reviewing workflow archives with --archive, container specs with --containerize, and between-workflow output caching with SNAKEMAKE_OUTPUT_CACHE / --cache.

Start with

• Deployment commands and directive patterns: references/deployment-reference.md.
• Storage provider and filesystem behavior: references/storage-reference.md.
• Failure diagnosis and recovery checklists: references/troubleshooting.md.
• Jobscript property inspection: run python scripts/inspect_job_properties.py --help.

Boundaries

• General CLI construction, target selection, profiles, and core execution planning belong to the root skill or command/execution sub-skills.
• Python API and plugin authoring details belong to ../python-api-plugins/SKILL.md.
• Reports, linting, benchmark interpretation, and test debugging belong to ../debugging-reporting/SKILL.md.
• Language syntax for ordinary rules, wildcards, inputs, and outputs belongs outside this sub-skill unless it directly affects deployment or storage behavior.

Snakemake 9.23.1 cautions

• Prefer --software-deployment-method conda apptainer (or --sdm conda apptainer) over older mental models that treat deployment flags as unrelated toggles.
• --use-conda, --use-apptainer / --use-singularity, and --use-envmodules remain accepted convenience flags for the corresponding deployment methods.
• Do not suggest --reason; it is not a valid Snakemake 9.23.1 flag, although dry-run output still reports reasons for jobs.
• External tools and plugins are not bundled by Snakemake itself: conda, Apptainer/Singularity, storage plugins, executor plugins, credentials, and cluster/cloud commands must be present in the target runtime.