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.
updateDataPackages(bioc_data_packages, pkg, ...)	Update the bioc_data_packages json file, adding/updating: pkg: { urls: [urls], md5: md5, fn: tarball }
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

exception bioconda_utils.bioconductor_skeleton.PageNotFoundError

bioconda_utils.bioconductor_skeleton.bioconductor_versions()

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

bioconda_utils.bioconductor_skeleton.latest_bioconductor_release_version()

Latest Bioconductor release version.

bioconda_utils.bioconductor_skeleton.latest_bioconductor_devel_version()

Latest Bioconductor version in development.

bioconda_utils.bioconductor_skeleton.bioconductor_tarball_url(package, pkg_version, bioc_version)

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_annotation_data_url(package, pkg_version, bioc_version)

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)

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.bioarchive_url(package, pkg_version, bioc_version=None)

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.cargoport_url(package, pkg_version, bioc_version=None)

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.find_best_bioc_version(package, version)

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

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

bioconda_utils.bioconductor_skeleton.fetchPackages(bioc_version)

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.packagesNeedingX(packages)

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_recursive(proj, seen_dependencies, recipe_dir, config, bioc_data_packages, force, bioc_version, pkg_version, versioned, recursive)

Parameters:

• proj (BioCProjectPage object) –

• seen_dependencies (list) – Dependencies to ignore

• recipe_dir (str) – Path to recipe dir

• config (str) – Path to recipes config file

• bioc_data_packages (str) – Path to the bioc_data_packages recipe, which stores the URL and MD5 of all bioconductor packages across versions

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

bioconda_utils.bioconductor_skeleton.updateDataPackages(bioc_data_packages, pkg, urls, md5, tarball)

Update the bioc_data_packages json file, adding/updating: pkg: {

urls: [urls], md5: md5, fn: tarball

}

bioconda_utils.bioconductor_skeleton.write_recipe(package, recipe_dir, config, bioc_data_packages=None, 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)

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. In that case also update bioconductor-data-packages.

Parameters:

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

• recipe_dir (str) –

• config (str or dict) –

• bioc_data_packages (str) – Path to the bioc_data_packages recipe, which stores the URL and MD5 of all bioconductor packages across versions

• 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.