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update bcbioR version
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lpantano committed Oct 31, 2024
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Expand Up @@ -17,15 +17,15 @@ Go to each analysis-type section to learn how to use our platform.
* When the session is started, set you library path typing this command in your console Rstudio window: `.libPaths("/n/app/bcbio/R4.3.1_rnaseq")`

* Load bcbioR with `library(bcbioR)`
* 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
* Make sure the version is 0.3.0 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

## General Project

Use the [hcbc app](https://hcbc.connect.hms.harvard.edu/content/8cd62872-0ec9-4905-8920-c745d2375758) to set up projects names. This name will be used for O2/FAS/github and dropbox. They may be already defined in the Trello card.

This set up needs [bcbioR](https://github.com/bcbio/bcbioR) and [usethis](https://usethis.r-lib.org) packages.

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
Make sure the version is `0.3.0` 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

* Create an R Project located in 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")`
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