add chipseq o2 library

docs/devops.md

@@ -35,6 +35,26 @@ options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor
 options(repos = c(CRAN = "https://packagemanager.posit.co/cran/2024-05-01"))
 ```
 
+### Creating env in Data Studio
+
+Set up the package manager [properly](https://packagemanager.posit.co/client/#/repos/bioconductor/setup?distribution=ubuntu-22.04):
+
+```
+# Configure BioCManager to use Posit Package Manager:
+options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/latest")
+options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/latest/config.yaml")
+
+# Configure a CRAN snapshot compatible with Bioconductor 3.20:
+options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))
+install.packages("BiocManager")
+```
+
+Install minimum system library packages from [ubuntu22](ubuntu22.system.ready.txt).
+
+Install all needed packages, and stop the server to get the first checkpoint with the packages installed. 
+
+After this, other users can start a new DataStudio from it with the dependencies already installed.
+
 ### Installing sc packages in O2
 
 ### CELLCHAT

docs/index.md

@@ -44,7 +44,11 @@ If you want to push this project to GitHub, follow these steps:
 
 ## scRNAseq
 
-Please, change to this common library path to perform you  analysis: `.libPaths("/n/app/bcbio/R4.3.1_singlecell/")`.
+Please, change to this common library path to perform you  analysis: `.libPaths("/n/app/bcbio/R4.3.1_singlecell")`.
+
+## ChipSeq
+
+Please, change to this common library path to perform you  analysis: `.libPaths("/n/app/bcbio/R4.3.1_chipseq")`.
 
 # bcbioR supported templates
 

docs/ubuntu22.system.ready.txt

@@ -0,0 +1,20 @@
+
+R CMD javareconf
+apt-get install -y bwidget
+apt-get install -y default-jdk
+apt-get install -y git
+apt-get install -y gsfonts
+apt-get install -y imagemagick
+apt-get install -y jags
+apt-get install -y libcurl4-openssl-dev
+apt-get install -y libeigen3-dev
+apt-get install -y libglpk-dev
+apt-get install -y libgsl0-dev
+apt-get install -y libhiredis-dev
+apt-get install -y libmagick++-dev
+apt-get install -y libopenbabel-dev
+apt-get install -y libssl-dev
+apt-get install -y libxml2-dev
+apt-get install -y make
+apt-get install -y ocl-icd-opencl-dev
+apt-get install -y pandoc