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JetBrains Research License license Tests Linux tests Tests Windows tests

SnakeCharm SnakeCharm

About

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 in Settings | Languages & Frameworks | Snakemake. Snakemake framework should be configured to use python interpreter with snakemake module installed.

Features available in Snakefile and *.smk, *.rule, *.rules files:

  • Python code syntax highlighting

  • Snakemake specific syntax highlighting

    • Highlight rule section names
    • Syntax highlighting for Snakemake string format language, e.g. in strings like "results/sample_{genome}.bam".
    • Special highlighting for rule wildcards and their usages

  • Code completion and goto to declaration for:

    • Snakemake specific variables (e.g. config, rules, etc);
    • Snakemake api methods like expand, temp, etc.
    • Rules names after rules., checkpoints after checkpoints.
    • Rules sections names after rules.my_rule_name.
    • Rule sections keywords arguments, e.g. after rules.my_rule_name.input.
    • Wildcards and sections names in shell, input, message, params and other sections
    • Paths in sections: configfile, workdir, conda, include.
    • Completion for wrappers names in wrapper: sections
    • Wrappers with detailed meta.yaml provides completion for rule section keyword arguments in output, input, params sections
    • Python methods and variables

  • Structure 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:

Installation

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):

  • Open IDEA/PyCharm Preferences
  • Choose Plugins section
  • Press gear icon and choose Install Plugin from Disk...
  • Use *.zip bundle download from Plugin Manager or built from sources

Setup Snakemake support

To 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

IntelliJ Plugins Repository

Plugin is available in IntelliJ Plugins Repository, see SnakeCharm Plugin.

EAP Updates

Early builds of coming releases are available in EAP channel. To receive this updates add EAP repository:

  • Open PyCharm / IntelliJ IDEA IDE settings
  • In Plugins section press ⚙️ (gear icon), select Manage Plugin Repositories...
  • Add repo https://plugins.jetbrains.com/plugins/eap/list using + button, press OK (Complete guide at Custom Release Channels)
  • Switch to Marketplace tab, search for snakecharm
  • EAP builds will be visible as plugin updates if compatible with your IDE build

Support

Contact me at roman.chernyatchik@jetbrains.com or post issues in Issue Tracker

Development

Pull requests are welcome. It is my side project, so I appreciate your help with implementation of desired features. See DEVELPER.md