kb_python.compile
¶
Module Contents¶
Functions¶
Get the tag name of the latest GitHub release, given a url to the |
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Fetch the filename from a URL. |
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Get the tarball url of the specified or latest kallisto release. |
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Get the tarball url of the specified or latest bustools release. |
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Find the root directory of a git repo by walking. |
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Compile kallisto from source. |
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Compile bustools from source. |
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Compile kallisto and/or bustools binaries by downloading and compiling |
- exception kb_python.compile.CompileError¶
Bases:
Exception
Common base class for all non-exit exceptions.
- kb_python.compile.get_latest_github_release_tag(releases_url: str) str ¶
Get the tag name of the latest GitHub release, given a url to the releases API.
- Parameters
releases_url – Url to the releases API
- Returns
The tag name
- kb_python.compile.get_filename_from_url(url: str) str ¶
Fetch the filename from a URL.
- Parameters
url – The url
- Returns
The filename
- kb_python.compile.get_kallisto_url(ref: Optional[str] = None) str ¶
Get the tarball url of the specified or latest kallisto release.
- Parameters
ref – Commit or release tag, defaults to None. By default, the most recent release is used.
- Returns
Tarball url
- kb_python.compile.get_bustools_url(ref: Optional[str] = None) str ¶
Get the tarball url of the specified or latest bustools release.
- Parameters
ref – Commit or release tag, defaults to None. By default, the most recent release is used.
- Returns
Tarball url
- kb_python.compile.find_git_root(path: str) str ¶
Find the root directory of a git repo by walking.
- Parameters
path – Path to start the search
- Returns
Path to root of git repo
- Raises
CompileError – If the git root could not be found
- kb_python.compile.compile_kallisto(source_dir: str, binary_path: str, cmake_arguments: Optional[str] = None) str ¶
Compile kallisto from source.
- Parameters
source_dir – Path to directory containing root of kallisto git repo
binary_path – Path to place compiled binary
cmake_arguments – Additional arguments to pass to the cmake command
- Returns
Path to compiled binary
- kb_python.compile.compile_bustools(source_dir: str, binary_path: str, cmake_arguments: Optional[str] = None) str ¶
Compile bustools from source.
- Parameters
source_dir – Path to directory containing root of bustools git repo
binary_path – Path to place compiled binary
cmake_arguments – Additional arguments to pass to the cmake command
- Returns
Path to compiled binary
- kb_python.compile.compile(target: typing_extensions.Literal[kallisto, bustools, all], out_dir: Optional[str] = None, cmake_arguments: Optional[str] = None, url: Optional[str] = None, ref: Optional[str] = None, overwrite: bool = False, temp_dir: str = 'tmp') Dict[str, str] ¶
Compile kallisto and/or bustools binaries by downloading and compiling a source archive.
- Parameters
target – Which binary to compile. May be one of kallisto, bustools or all
out_dir – Path to output directory, defaults to None
cmake_arguments – Additional arguments to pass to the cmake command
url – Download the source archive from this url instead, defaults to None
ref – Commit hash or tag to use, defaults to None
overwrite – Overwrite any existing results, defaults to False
temp_dir – Path to temporary directory, defaults to tmp
- Returns
Dictionary of results