diff --git a/docs/index.md b/docs/index.md index 307371f..fe784fa 100644 --- a/docs/index.md +++ b/docs/index.md @@ -8,6 +8,17 @@ We are developing platforms for each analysis type we have experience with at HC Go to each analysis type section to learn how to use our platform. +## Set up package + +* Using O2 open OnDemand: + * Remove `bcbio` from you `PATH` by commenting the line in your `.bashrc` if you have it + * Start Rstudio With these modules on: `gcc/9.2.0 imageMagick/7.1.0 geos/3.10.2 cmake/3.22.2 R/4.3.1 fftw/3.3.10 gdal/3.1.4 udunits/2.2.28 boost/1.75.0` + * When the session is started, set you library path typing this command in your console Rstudio window: `.libPaths("/n/app/bcbio/R4.3.1")` + +* 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 + + ## General Project This set up needs `bcbioR` and `usethis` packages. @@ -23,13 +34,6 @@ Make sure the version is 0.1.3 with this command `packageVersion("bcbioR")` or r ## RNAseq -* Using O2 open OnDemand: - * Remove `bcbio` from you `PATH` by commenting the line in your `.bashrc` if you have it - * Start Rstudio With these modules on: `gcc/9.2.0 imageMagick/7.1.0 geos/3.10.2 cmake/3.22.2 R/4.3.1 fftw/3.3.10 gdal/3.1.4 udunits/2.2.28 boost/1.75.0` - * When the session is started, set you library path typing this command in your console Rstudio window: `.libPaths("/n/app/bcbio/R4.3.1")` - -* 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 * Follow this instruction https://bcbio.github.io/bcbioR/#set-base-project to start you project * Follow this instruction https://bcbio.github.io/bcbioR/#set-rnaseq-report-folder to start your RNAseq analysis