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Update index.md
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abartlett004 authored Jun 27, 2024
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Expand Up @@ -25,8 +25,8 @@ This set up needs [bcbioR](https://github.com/bcbio/bcbioR) and [usethis](https:

Make sure the version is `0.1.3` with this command `packageVersion("bcbioR")` or re-install with `devtools::install_github("bcbio/bcbioR",build_manual = TRUE, build_vignettes = TRUE)`, if you are in your own environment

* Deploy folders/files compatible with any project: `bcbioR::bcbio_templates(type="base", outpath="/path/to/analysis/folder")`
* Activate your R session to make your working directory to be your project folder: `usethis::proj_activate("/path/to/analysis/folder")`
* Deploy folders/files compatible with any project: `bcbioR::bcbio_templates(type="base", outpath="/path/to/analysis/folder")`
* Start a git repository: `usethis::use_git()`
* Only once every 30 days, set up your github credentials: `usethis::gh_token_help()`
* **NOTE** You may want to run this first to keep this token working in future sessions: `git config --global credential.helper store`
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