kb_python.config
¶
Module Contents¶
Functions¶
Finds platform-dependent kallisto binary included with the installation. |
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Finds platform-dependent bustools binary included with the installation. |
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Dummy function that simply returns the current value of KALLISTO_PATH. |
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Dummy function that simply returns the current value of BUSTOOLS_PATH. |
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Helper function to set the KALLISTO_PATH variable. Automatically finds the |
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Helper function to set the BUSTOOLS_PATH variable. Automatically finds the |
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Set this run to be a dry run. |
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Return whether the current run is a dry run. |
Turn off validation. |
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Return whether validation is turned on. |
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kb_python.config.
PACKAGE_PATH
¶
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kb_python.config.
PLATFORM
¶
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kb_python.config.
BINS_DIR
= bins¶
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kb_python.config.
TEMP_DIR
= tmp¶
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kb_python.config.
DRY
= False¶
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kb_python.config.
VALIDATE
= True¶
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kb_python.config.
CHUNK_SIZE
¶
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kb_python.config.
get_provided_kallisto_path
()¶ Finds platform-dependent kallisto binary included with the installation.
- Returns
path to the binary, None if not found
- Return type
str
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kb_python.config.
get_provided_bustools_path
()¶ Finds platform-dependent bustools binary included with the installation.
- Returns
path to the binary, None if not found
- Return type
str
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kb_python.config.
KALLISTO_PATH
¶
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kb_python.config.
BUSTOOLS_PATH
¶
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kb_python.config.
Technology
¶
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kb_python.config.
WHITELIST_DIR
= whitelists¶
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kb_python.config.
MAP_DIR
= maps¶
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kb_python.config.
TECHNOLOGIES
¶
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kb_python.config.
TECHNOLOGIES_MAPPING
¶
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kb_python.config.
Reference
¶
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kb_python.config.
REFERENCES
¶
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kb_python.config.
REFERENCES_MAPPING
¶
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exception
kb_python.config.
UnsupportedOSException
¶ Bases:
Exception
Common base class for all non-exit exceptions.
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exception
kb_python.config.
NotExecutableException
¶ Bases:
Exception
Common base class for all non-exit exceptions.
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kb_python.config.
get_kallisto_binary_path
()¶ Dummy function that simply returns the current value of KALLISTO_PATH.
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kb_python.config.
get_bustools_binary_path
()¶ Dummy function that simply returns the current value of BUSTOOLS_PATH.
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kb_python.config.
set_kallisto_binary_path
(path)¶ Helper function to set the KALLISTO_PATH variable. Automatically finds the full path to the executable and sets that as KALLISTO_PATH.
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kb_python.config.
set_bustools_binary_path
(path)¶ Helper function to set the BUSTOOLS_PATH variable. Automatically finds the full path to the executable and sets that as BUSTOOLS_PATH.
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kb_python.config.
set_dry
()¶ Set this run to be a dry run.
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kb_python.config.
is_dry
()¶ Return whether the current run is a dry run.
- Returns
whether the current run is a dry run
- Return type
bool
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kb_python.config.
no_validate
()¶ Turn off validation.
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kb_python.config.
is_validate
()¶ Return whether validation is turned on.
- Returns
whether validation is on
- Return type
bool