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.
`packagesNeedingX`(packages)	Return a set of all packages needing X.
`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.packagesNeedingX(packages)[source]¶: Return a set of all packages needing X. Packages needing X are defines as those that directly or indirectly require rgl.

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, needs_x=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.
needs_x (bool or None) – If None, we need to determine if this requires X and therefore additional build dependencies and test environment variables.

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.