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feat: add aria2c wrapper #2725

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feat: add aria2c wrapper #2725

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fgvieira
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@fgvieira fgvieira commented Mar 7, 2024

Add wrapper for aria2c, since it allows (among others):

  • download of several protocols (e.g. HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink)
  • parallel downloads
  • automated checksum check
  • pre-allocate disk space

QC

  • I confirm that:

For all wrappers added by this PR,

  • there is a test case which covers any introduced changes,
  • input: and output: file paths in the resulting rule can be changed arbitrarily,
  • either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
  • rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
  • all environment.yaml specifications follow the respective best practices,
  • the environment.yaml pinning has been updated by running snakedeploy pin-conda-envs environment.yaml on a linux machine,
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
  • all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
  • stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
  • temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
  • the meta.yaml contains a link to the documentation of the respective tool or command,
  • Snakefiles pass the linting (snakemake --lint),
  • Snakefiles are formatted with snakefmt,
  • Python wrapper scripts are formatted with black.
  • Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

@fgvieira
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fgvieira commented May 29, 2024

I've included the functionparse_input for testing, but the idea is to move it to snakemake as a helper function, no? If so, will you do it or should I open a PR?

On another issue, one test is currently disabled since snakemake-storage-plugin-http is not available in the test environment. Should we leave it as-is (to keep the two repos tests separate), or will you enable it?

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