change order

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