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galaxy.tool_util.deps.mulled package

Submodules

galaxy.tool_util.deps.mulled.mulled_build module

Build a mulled image for specified conda targets.

Examples

Build a mulled image with:

mulled-build build ‘samtools=1.3.1–4,bedtools=2.22’

galaxy.tool_util.deps.mulled.mulled_build.main(argv=None)

Main entry-point for the CLI tool.

galaxy.tool_util.deps.mulled.mulled_build_channel module

Build a mulled images for all recent conda recipe updates that don’t have existing images.

Examples:

Build mulled images for recent bioconda changes with:

mulled-build-channel build

Build, test, and publish images with the follow command:

mulled-build-channel all

See recent changes that would be built with:

mulled-build-channel list

galaxy.tool_util.deps.mulled.mulled_build_channel.main(argv=None)

Main entry-point for the CLI tool.

galaxy.tool_util.deps.mulled.mulled_build_files module

Build all composite mulled recipes discovered in TSV files.

Use mulled-build-channel to build images for single recipes for a whole conda channel. This script instead builds images for combinations of recipes. This script can be given a single TSV file or a directory of TSV files to process.

Examples:

Build all recipes discovered in tsv files in a single directory.

mulled-build-files build

galaxy.tool_util.deps.mulled.mulled_build_files.main(argv=None)

Main entry-point for the CLI tool.

galaxy.tool_util.deps.mulled.mulled_build_tool module

Build a mulled images for a tool source (Galaxy or CWL tool).

Examples:

Build mulled images for requirements defined in a tool:

mulled-build-tool build path/to/tool_file.xml

galaxy.tool_util.deps.mulled.mulled_build_tool.main(argv=None)

Main entry-point for the CLI tool.

galaxy.tool_util.deps.mulled.mulled_build_tool.requirements_to_mulled_targets(requirements)

Convert Galaxy’s representation of requirements into mulled Target objects.

Only package requirements are retained.

galaxy.tool_util.deps.mulled.mulled_search module

class galaxy.tool_util.deps.mulled.mulled_search.QuaySearch(organization)

Bases: object

Tool to search within a quay organization for a given software name.

__init__(organization)

build_index()

Create an index to quickly examine the repositories of a given quay.io organization.

search_repository(search_string, non_strict)

Search Docker containers on quay.io. Results are displayed with all available versions, including the complete image name.

get_additional_repository_information(repository_string)

Function downloads additional information from quay.io to get the tag-field which includes the version number.

class galaxy.tool_util.deps.mulled.mulled_search.CondaSearch(channel)

Bases: object

Tool to search the bioconda channel

__init__(channel)

get_json(search_string)

Function takes search_string variable and returns results from the bioconda channel in JSON format

class galaxy.tool_util.deps.mulled.mulled_search.GitHubSearch

Bases: object

Tool to search the GitHub bioconda-recipes repo

get_json(search_string)

Takes search_string variable and return results from the bioconda-recipes github repository in JSON format

process_json(json, search_string)

Take JSON input and process it, returning the required data

recipe_present(search_string)

Check if a recipe exists in bioconda-recipes which matches search_string exactly

galaxy.tool_util.deps.mulled.mulled_search.get_package_hash(packages, versions)

Take packages and versions (if the latter are given) and returns a hash for each. Also checks github to see if the container is already present.

galaxy.tool_util.deps.mulled.mulled_search.singularity_search(search_string)

Check if a singularity package is present and return the link.

galaxy.tool_util.deps.mulled.mulled_search.readable_output(json, organization='biocontainers', channel='bioconda')

galaxy.tool_util.deps.mulled.mulled_search.main(argv=None)

galaxy.tool_util.deps.mulled.util module

Utilities for working with mulled abstractions outside the mulled package.

galaxy.tool_util.deps.mulled.util.quay_versions(namespace, pkg_name)

Get all version tags for a Docker image stored on quay.io for supplied package name.

galaxy.tool_util.deps.mulled.util.mulled_tags_for(namespace, image, tag_prefix=None, resolution_cache=None)

Fetch remote tags available for supplied image name.

The result will be sorted so newest tags are first.

galaxy.tool_util.deps.mulled.util.split_tag(tag)

Split mulled image tag into conda version and conda build.

galaxy.tool_util.deps.mulled.util.version_sorted(elements)

Sort iterable based on loose description of “version” from newest to oldest.

class galaxy.tool_util.deps.mulled.util.Target(package_name, version, build, package)

Bases: tuple

build

Alias for field number 2

package

Alias for field number 3

package_name

Alias for field number 0

version

Alias for field number 1

galaxy.tool_util.deps.mulled.util.build_target(package_name, version=None, build=None, tag=None)

Use supplied arguments to build a Target object.

galaxy.tool_util.deps.mulled.util.conda_build_target_str(target)

galaxy.tool_util.deps.mulled.util.v1_image_name(targets, image_build=None, name_override=None)

Generate mulled hash version 1 container identifier for supplied arguments.

If a single target is specified, simply use the supplied name and version as the repository name and tag respectively. If multiple targets are supplied, hash the package names and versions together as the repository name. For mulled version 1 containers the image build is the repository tag (if supplied).

>>> single_targets = [build_target("samtools", version="1.3.1")]
>>> v1_image_name(single_targets)
'samtools:1.3.1'
>>> multi_targets = [build_target("samtools", version="1.3.1"), build_target("bwa", version="0.7.13")]
>>> v1_image_name(multi_targets)
'mulled-v1-b06ecbd9141f0dbbc0c287375fc0813adfcbdfbd'
>>> multi_targets_on_versionless = [build_target("samtools", version="1.3.1"), build_target("bwa")]
>>> v1_image_name(multi_targets_on_versionless)
'mulled-v1-bda945976caa5734347fbf7f35066d9f58519e0c'
>>> multi_targets_versionless = [build_target("samtools"), build_target("bwa")]
>>> v1_image_name(multi_targets_versionless)
'mulled-v1-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'

galaxy.tool_util.deps.mulled.util.v2_image_name(targets, image_build=None, name_override=None)

Generate mulled hash version 2 container identifier for supplied arguments.

If a single target is specified, simply use the supplied name and version as the repository name and tag respectively. If multiple targets are supplied, hash the package names as the repository name and hash the package versions (if set) as the tag.

>>> single_targets = [build_target("samtools", version="1.3.1")]
>>> v2_image_name(single_targets)
'samtools:1.3.1'
>>> single_targets = [build_target("samtools", version="1.3.1", build="py_1")]
>>> v2_image_name(single_targets)
'samtools:1.3.1--py_1'
>>> single_targets = [build_target("samtools", version="1.3.1")]
>>> v2_image_name(single_targets, image_build="0")
'samtools:1.3.1'
>>> single_targets = [build_target("samtools", version="1.3.1", build="py_1")]
>>> v2_image_name(single_targets, image_build="0")
'samtools:1.3.1--py_1'
>>> multi_targets = [build_target("samtools", version="1.3.1"), build_target("bwa", version="0.7.13")]
>>> v2_image_name(multi_targets)
'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:4d0535c94ef45be8459f429561f0894c3fe0ebcf'
>>> multi_targets_on_versionless = [build_target("samtools", version="1.3.1"), build_target("bwa")]
>>> v2_image_name(multi_targets_on_versionless)
'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:b0c847e4fb89c343b04036e33b2daa19c4152cf5'
>>> multi_targets_versionless = [build_target("samtools"), build_target("bwa")]
>>> v2_image_name(multi_targets_versionless)
'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'

galaxy.tool_util.deps.mulled.util.split_container_name(name)

Takes a container name (e.g. samtools:1.7–1) and returns a list (e.g. [‘samtools’, ‘1.7’, ‘1’]) >>> split_container_name(‘samtools:1.7–1’) [‘samtools’, ‘1.7’, ‘1’]

galaxy.tool_util.deps.mulled.util.image_name(targets, image_build=None, name_override=None)

Generate mulled hash version 1 container identifier for supplied arguments.

If a single target is specified, simply use the supplied name and version as the repository name and tag respectively. If multiple targets are supplied, hash the package names and versions together as the repository name. For mulled version 1 containers the image build is the repository tag (if supplied).

>>> single_targets = [build_target("samtools", version="1.3.1")]
>>> v1_image_name(single_targets)
'samtools:1.3.1'
>>> multi_targets = [build_target("samtools", version="1.3.1"), build_target("bwa", version="0.7.13")]
>>> v1_image_name(multi_targets)
'mulled-v1-b06ecbd9141f0dbbc0c287375fc0813adfcbdfbd'
>>> multi_targets_on_versionless = [build_target("samtools", version="1.3.1"), build_target("bwa")]
>>> v1_image_name(multi_targets_on_versionless)
'mulled-v1-bda945976caa5734347fbf7f35066d9f58519e0c'
>>> multi_targets_versionless = [build_target("samtools"), build_target("bwa")]
>>> v1_image_name(multi_targets_versionless)
'mulled-v1-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'