bioconductor_skeleton¶
Conda Skeleton for Bioconductor Recipes
Functions
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Constructs a url for the package as archived on bioaRchive |
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Constructs a url for an annotation package tarball |
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Constructs a url for an experiment data package tarball |
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Constructs a url for a package tarball |
Returns a list of available Bioconductor versions scraped from the Bioconductor site. |
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Constructs a url for the package as archived on the galaxy cargo-port |
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Return a dictionary of all bioconductor packages in a given release. |
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Given a package version number, identifies which BioC version[s] it is in and returns the latest. |
Latest Bioconductor version in development. |
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Latest Bioconductor release version. |
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Return a set of all packages needing X. |
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Write the meta.yaml and build.sh files. |
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Classes
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Represents a single Bioconductor package page and provides access to scraped data. |
Exceptions
Documentation
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bioconda_utils.bioconductor_skeleton.
bioarchive_url
(package, pkg_version, bioc_version=None)[source]¶ Constructs a url for the package as archived on bioaRchive
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bioconda_utils.bioconductor_skeleton.
bioconductor_annotation_data_url
(package, pkg_version, bioc_version)[source]¶ Constructs a url for an annotation package tarball
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bioconda_utils.bioconductor_skeleton.
bioconductor_experiment_data_url
(package, pkg_version, bioc_version)[source]¶ Constructs a url for an experiment data package tarball
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bioconda_utils.bioconductor_skeleton.
bioconductor_tarball_url
(package, pkg_version, bioc_version)[source]¶ Constructs a url for a package tarball
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bioconda_utils.bioconductor_skeleton.
bioconductor_versions
()[source]¶ Returns a list of available Bioconductor versions scraped from the Bioconductor site.
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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
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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}, ... }
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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) –
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bioconda_utils.bioconductor_skeleton.
latest_bioconductor_devel_version
()[source]¶ Latest Bioconductor version in development.
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bioconda_utils.bioconductor_skeleton.
latest_bioconductor_release_version
()[source]¶ Latest Bioconductor release version.
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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.
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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) –
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.