Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
License
Tests Linux
Tests Windows
SnakeCharm plugin for PyCharm / IntelliJ Platform IDEs adds IDE support for Snakemake workflows language, that is widely used in Bioinformatics. The plugin is developed by JetBrains Research Team, for more details see project home page.
Please report features suggestions or found bugs to project issue tracker.
Features highlights:
NB: To activate all features please enable
Snakemake
support inSettings | Languages & Frameworks | Snakemake
. Snakemake framework should be configured to use python interpreter withsnakemake
module installed.
Features available in Snakefile
and *.smk
, *.rule
, *.rules
files:
Python code syntax highlighting
Snakemake specific syntax highlighting
"results/sample_{genome}.bam"
.Code completion and goto to declaration for:
config
, rules
, etc);expand
, temp
, etc.rules.
, checkpoints after checkpoints.
rules.my_rule_name.
rules.my_rule_name.input.
shell
, input
, message
, params
and other sectionsconfigfile
, workdir
, conda
, include
.wrapper:
sectionsmeta.yaml
provides completion for rule section keyword arguments in output
, input
, params
sectionsStructure view for Snakemake files
Rules blocks folding
Open rule declaration by name using Navigate|Symbol...
Quick documentation for wrappers, that includes links to wrapper source code and paga in wrappers repository
Multiple code inspections for possible errors in snakemake files
Useful links:
Via JetBrains Plugins Market Place (recommended):
NB: If you've already configured custom file type for
Snakefile
or*.smk
files please delete it (or change file masks to smth else). Otherwise, your custom file type will replace SnakeCharm support in snakemake files.
In PyCharm (or other IntelliJ Platfrom
based IDE with Python Community Edition
plugin installed) open Preferences|Plugins|Marketplace|SnakeCharm
and press Install
button.
From ZIP plugin bundle (alternative way):
Plugins
sectionInstall Plugin from Disk...
*.zip
bundle download from Plugin Manager or built from sourcesTo enable all code insight features (e.g. code completion for directory
, touch
etc methods) please configure Python SDK with installed snakemake package.
https://github.com/JetBrains-Research/snakecharm/wiki#setup-snakemake-support
Plugin is available in IntelliJ Plugins Repository, see SnakeCharm Plugin.
Early builds of coming releases are available in EAP channel. To receive this updates add EAP repository:
PyCharm
/ IntelliJ IDEA
IDE settingsgear
icon), select Manage Plugin Repositories...
https://plugins.jetbrains.com/plugins/eap/list
using +
button, press OK
(Complete guide at Custom Release Channels)Marketplace
tab, search for snakecharm
Contact me at [email protected] or post issues in Issue Tracker
Pull requests are welcome. It is my side project, so I appreciate your help with implementation of desired features. See DEVELPER.md