bioconductor_skeleton

Conda Skeleton for Bioconductor Recipes

Functions

bioarchive_url(package, pkg_version[, …])

Constructs a url for the package as archived on bioaRchive

bioconductor_annotation_data_url(package, …)

Constructs a url for an annotation package tarball

bioconductor_experiment_data_url(package, …)

Constructs a url for an experiment data package tarball

bioconductor_tarball_url(package, …)

Constructs a url for a package tarball

bioconductor_versions()

Returns a list of available Bioconductor versions scraped from the Bioconductor site.

cargoport_url(package, pkg_version[, …])

Constructs a url for the package as archived on the galaxy cargo-port

fetchPackages(bioc_version)

Return a dictionary of all bioconductor packages in a given release.

find_best_bioc_version(package, version)

Given a package version number, identifies which BioC version[s] it is in and returns the latest.

latest_bioconductor_devel_version()

Latest Bioconductor version in development.

latest_bioconductor_release_version()

Latest Bioconductor release version.

write_recipe(package, recipe_dir, config[, …])

Write the meta.yaml and build.sh files.

write_recipe_recursive(proj, …)

param proj

Classes

BioCProjectPage(package[, bioc_version, …])

Represents a single Bioconductor package page and provides access to scraped data.

Exceptions

PackageNotFoundError

PageNotFoundError

Documentation

exception bioconda_utils.bioconductor_skeleton.PackageNotFoundError[source]

Bases: Exception

exception bioconda_utils.bioconductor_skeleton.PageNotFoundError[source]

Bases: Exception

bioconda_utils.bioconductor_skeleton.bioarchive_url(package, pkg_version, bioc_version=None)[source]

Constructs a url for the package as archived on bioaRchive

Parameters
  • package (str) – Case-sensitive Bioconductor package name

  • pkg_version (str) – Bioconductor package version

  • bioc_version (str) – Bioconductor release version. Not used;, only included for API compatibility with other url funcs

bioconda_utils.bioconductor_skeleton.bioconductor_annotation_data_url(package, pkg_version, bioc_version)[source]

Constructs a url for an annotation package tarball

Parameters
  • package (str) – Case-sensitive Bioconductor package name

  • pkg_version (str) – Bioconductor package version

  • bioc_version (str) – Bioconductor release version

bioconda_utils.bioconductor_skeleton.bioconductor_experiment_data_url(package, pkg_version, bioc_version)[source]

Constructs a url for an experiment data package tarball

Parameters
  • package (str) – Case-sensitive Bioconductor package name

  • pkg_version (str) – Bioconductor package version

  • bioc_version (str) – Bioconductor release version

bioconda_utils.bioconductor_skeleton.bioconductor_tarball_url(package, pkg_version, bioc_version)[source]

Constructs a url for a package tarball

Parameters
  • package (str) – Case-sensitive Bioconductor package name

  • pkg_version (str) – Bioconductor package version

  • bioc_version (str) – Bioconductor release version

bioconda_utils.bioconductor_skeleton.bioconductor_versions()[source]

Returns a list of available Bioconductor versions scraped from the Bioconductor site.

bioconda_utils.bioconductor_skeleton.cargoport_url(package, pkg_version, bioc_version=None)[source]

Constructs a url for the package as archived on the galaxy cargo-port

Parameters
  • package (str) – Case-sensitive Bioconductor package name

  • pkg_version (str) – Bioconductor package version

  • bioc_version (str) – Bioconductor release version. Not used;, only included for API compatibility with other url funcs

bioconda_utils.bioconductor_skeleton.fetchPackages(bioc_version)[source]

Return a dictionary of all bioconductor packages in a given release:

{package: {Version: "version",
           Depends: [list],
           Suggests: [list],
           MD5sum: "hash",
           License: "foo",
           Description: "Something...",
           NeedsCompilation: boolean},
          ...
}
bioconda_utils.bioconductor_skeleton.find_best_bioc_version(package, version)[source]

Given a package version number, identifies which BioC version[s] it is in and returns the latest.

If the package is not found, raises a PackageNotFound error.

Parameters
  • package – Case-sensitive Bioconductor package name

  • version – Bioconductor package version

  • None if no valid package found. (Returns) –

bioconda_utils.bioconductor_skeleton.latest_bioconductor_devel_version()[source]

Latest Bioconductor version in development.

bioconda_utils.bioconductor_skeleton.latest_bioconductor_release_version()[source]

Latest Bioconductor release version.

bioconda_utils.bioconductor_skeleton.write_recipe(package, recipe_dir, config, force=False, bioc_version=None, pkg_version=None, versioned=False, recursive=False, seen_dependencies=None, packages=None, skip_if_in_channels=None)[source]

Write the meta.yaml and build.sh files. If the package is detected to be a data package (bsed on the detected URL from Bioconductor), then also create a post-link.sh and pre-unlink.sh script that will download and install the package.

Parameters
  • package (str) – Bioconductor package name (case-sensitive)

  • recipe_dir (str) –

  • config (str or dict) –

  • force (bool) – If True, then recipes will get overwritten. If recursive is also True, all recipes created will get overwritten.

  • bioc_version (str) – Version of Bioconductor to target

  • pkg_version (str) – Force a particular package version

  • versioned (bool) – If True, then make a subdirectory for this version

  • recursive (bool) – If True, then also build any R or Bioconductor packages in the same recipe directory.

  • seen_dependencies (set) – Dependencies to skip and will be updated with any packages built by this function. Used internally when recursive=True.

  • packages (dict) – A dictionary, as returned by fetchPackages(), of all packages in a given bioconductor release and their versions.

  • skip_if_in_channels (list or None) – List of channels whose existing packages will be automatically added to seen_dependencies. Only has an effect if recursive=True.

bioconda_utils.bioconductor_skeleton.write_recipe_recursive(proj, seen_dependencies, recipe_dir, config, force, bioc_version, pkg_version, versioned, recursive)[source]
Parameters
  • proj (BioCProjectPage object) –

  • seen_dependencies (list) – Dependencies to ignore

  • recipe_dir (str) – Path to recipe dir

  • config (str) – Path to recipes config file

  • force (bool) – If True, any recipes that already exist will be overwritten.