snakecdysis
Installation
Install Snakecdysis python package
Requirement
Install the lastest release from PyPI - RECOMMENDED
Install the development version directly from the github repository
How to convert my snakemake workflow into a Python package combined to Snakecdysis ?
Generating the python package tree
Configuring your files
Transferring your snakemake workflow
update documentation comming soon
Package documentation
Snakecdysis package
snakecdysis.cli_wrapper Module
snakecdysis.snake_wrapper Module
Workflow functions
Install Module
Useful functions
Usefull functions
snakecdysis.useful_function Module
snakecdysis
Index
Edit on GitLab
Index
A
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C
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D
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E
|
F
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G
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I
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L
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M
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S
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T
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U
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V
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W
A
apptainer_url_files (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
C
check_and_download_apptainer() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
check_dir_or_string() (snakecdysis.snake_wrapper.SnakEcdysis method)
check_file_or_string() (snakecdysis.snake_wrapper.SnakEcdysis method)
check_privileges() (in module snakecdysis.useful_function)
clean_home() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
convert_genome_size() (in module snakecdysis.useful_function)
create_bash_completion() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
D
datatest_url_files (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
default_profile (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
description_tool (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
docs (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
download_url() (in module snakecdysis.useful_function)
DownloadProgressBar (class in snakecdysis.useful_function)
E
export_use_yaml (snakecdysis.snake_wrapper.SnakEcdysis attribute)
F
fail() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
G
get_active_profile (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
get_active_tools_path (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
get_config_value() (snakecdysis.snake_wrapper.SnakEcdysis method)
get_dir() (in module snakecdysis.useful_function)
get_epilog() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
get_files_ext() (in module snakecdysis.useful_function)
get_files_ext2() (in module snakecdysis.useful_function)
get_last_version() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
get_tool_configfile() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
git_configfile_path (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
git_tools_path (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
git_url (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
I
install_mode (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
install_path (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
L
latest_version (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
M
main_wrapper() (in module snakecdysis.cli_wrapper)
module
snakecdysis
,
[1]
snakecdysis.cli_wrapper
snakecdysis.snake_wrapper
snakecdysis.useful_function
multiprocessing_download() (in module snakecdysis.useful_function)
S
set_config_value() (snakecdysis.snake_wrapper.SnakEcdysis method)
snakecdysis
module
,
[1]
SnakEcdysis (class in snakecdysis.snake_wrapper)
snakecdysis.cli_wrapper
module
snakecdysis.snake_wrapper
module
snakecdysis.useful_function
module
snakecdysis_version (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
snakefile (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
SnakeInstaller (class in snakecdysis.snake_wrapper)
snakemake_scripts (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
soft_name (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
sort_human() (in module snakecdysis.useful_function)
string_to_dag (snakecdysis.snake_wrapper.SnakEcdysis attribute)
T
tools_mode (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
tools_version_to_df() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)
U
update_to() (snakecdysis.useful_function.DownloadProgressBar method)
user_profile_config (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
user_tools_path (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
V
var_2_bool() (in module snakecdysis.useful_function)
version (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
W
write_config() (snakecdysis.snake_wrapper.SnakEcdysis method)
write_user_tools_path() (snakecdysis.snake_wrapper.SnakEcdysis method)
(snakecdysis.snake_wrapper.SnakeInstaller method)