snakecdysis
latest
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
API
snakecdysis
create_config
edit_cluster_config
edit_tools
install_cluster
install_local
run_cluster
run_local
show_tools
test_install
snakecdysis
Index
Edit on GitLab
Index
Symbols
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A
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C
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D
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E
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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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P
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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
Symbols
--bash_completion
PKGNAME-install_cluster command line option
PKGNAME-install_local command line option
snakecdysis-install_cluster command line option
snakecdysis-install_local command line option
--config
snakecdysis-run_cluster command line option
snakecdysis-run_local command line option
--configyaml
snakecdysis-create_config command line option
--data_dir
snakecdysis-test_install command line option
--env
PKGNAME-install_cluster command line option
snakecdysis-install_cluster command line option
--install_env
snakecdysis command line option
--no-bash_completion
PKGNAME-install_cluster command line option
PKGNAME-install_local command line option
snakecdysis-install_cluster command line option
snakecdysis-install_local command line option
--pdf
snakecdysis-run_cluster command line option
snakecdysis-run_local command line option
--restore
snakecdysis command line option
snakecdysis-edit_tools command line option
--scheduler
PKGNAME-install_cluster command line option
snakecdysis-install_cluster command line option
--threads
snakecdysis-run_local command line option
--version
snakecdysis command line option
-c
snakecdysis-create_config command line option
snakecdysis-run_cluster command line option
snakecdysis-run_local command line option
-d
snakecdysis-test_install command line option
-e
PKGNAME-install_cluster command line option
snakecdysis command line option
snakecdysis-install_cluster command line option
-p
snakecdysis-run_local command line option
-pdf
snakecdysis-run_cluster command line option
-r
snakecdysis command line option
snakecdysis-edit_tools command line option
-s
PKGNAME-install_cluster command line option
snakecdysis-install_cluster command line option
-t
snakecdysis-run_local command line option
-v
snakecdysis command line option
A
args_cluster_config (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
args_tools_path (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
C
check_and_download_singularity() (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_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_config_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)
P
PKGNAME-install_cluster command line option
--bash_completion
--env
--no-bash_completion
--scheduler
-e
-s
PKGNAME-install_local command line option
--bash_completion
--no-bash_completion
S
set_config_value() (snakecdysis.snake_wrapper.SnakEcdysis method)
singularity_url_files (snakecdysis.snake_wrapper.SnakEcdysis attribute)
(snakecdysis.snake_wrapper.SnakeInstaller attribute)
snakecdysis
module
,
[1]
SnakEcdysis (class in snakecdysis.snake_wrapper)
snakecdysis command line option
--install_env
--restore
--version
-e
-r
-v
snakecdysis-create_config command line option
--configyaml
-c
snakecdysis-edit_tools command line option
--restore
-r
snakecdysis-install_cluster command line option
--bash_completion
--env
--no-bash_completion
--scheduler
-e
-s
snakecdysis-install_local command line option
--bash_completion
--no-bash_completion
snakecdysis-run_cluster command line option
--config
--pdf
-c
-pdf
SNAKEMAKE_OTHER
snakecdysis-run_local command line option
--config
--pdf
--threads
-c
-p
-t
SNAKEMAKE_OTHER
snakecdysis-test_install command line option
--data_dir
-d
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_OTHER
snakecdysis-run_cluster command line option
snakecdysis-run_local command line option
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_cluster_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)
Read the Docs
v: latest
Versions
latest
0.1.0
0.0.5
0.0.4
0.0.3
0.0.1
0.0.1-rc
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