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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Update the bioc_data_packages json file, adding/updating: pkg: { urls: [urls], md5: md5, fn: tarball } |
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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
- bioconda_utils.bioconductor_skeleton.bioconductor_versions()[source]¶
Returns a list of available Bioconductor versions scraped from the Bioconductor site.
- bioconda_utils.bioconductor_skeleton.latest_bioconductor_release_version()[source]¶
Latest Bioconductor release version.
- bioconda_utils.bioconductor_skeleton.latest_bioconductor_devel_version()[source]¶
Latest Bioconductor version in development.
- bioconda_utils.bioconductor_skeleton.bioconductor_tarball_url(package, pkg_version, bioc_version)[source]¶
Constructs a url for a package tarball
- bioconda_utils.bioconductor_skeleton.bioconductor_annotation_data_url(package, pkg_version, bioc_version)[source]¶
Constructs a url for an annotation package tarball
- bioconda_utils.bioconductor_skeleton.bioconductor_experiment_data_url(package, pkg_version, bioc_version)[source]¶
Constructs a url for an experiment data package tarball
- bioconda_utils.bioconductor_skeleton.bioarchive_url(package, pkg_version, bioc_version=None)[source]¶
Constructs a url for the package as archived on bioaRchive
- 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
- 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
found. (Returns None if no valid package) –
- 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.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_recursive(proj, seen_dependencies, recipe_dir, config, bioc_data_packages, 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
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)[source]¶
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)[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. In that case also update bioconductor-data-packages.
- Parameters:
package (str) – Bioconductor package name (case-sensitive)
recipe_dir (str) –
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.