This is an RStudio addin that serves as a lighweight frontend to the Snakemaker VSCode backend, to generate snakemake workflow using either bash or R commands.
install.packages("devtools")
devtools::install_github("molinerisLab/Rsnkmaker")
In order to launch the addin: Select the Addin in the RStudio menu, then select "Snakemaker"
The addin will open as a shiny app in the viewer page in the right part of the RStudio interface in a non blocking way, allowing the user to continue using the console and perform operations on it while the addin is running.
The main panel display existing commands from the history (Bash OR R) and automatically updates as new lines are parsed from either the Terminal or R Console. Each line can be edited directly within the viewer using the edit button located on the right side of each entry. Users can start or stop the recording of commands parsed from the console or terminal, using the icon present on the top, left-side of the settings. When recording is active, only the commands executed during that period will be stored and displayed in the addin’s history panel.
- Choose the history to display (either bash or R)
- Modify the local port used to send parsed commands so that it matches the one the VSCode Snakemake extension is listening on
Rules can be generated from the entire stored history using the “Generate” button, or from a subset of selected lines using “Generate from Selection” History lines can be removed from the view by selecting them and clicking the trashcan icon. Commands used to generate rules are automatically moved from the active history to the archived lines panel. Users can save the current history to a local file or import existing commands into the addin using the “Import” button.