diff --git a/docs/devops.md b/docs/devops.md index 4cde88a..5333975 100644 --- a/docs/devops.md +++ b/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 diff --git a/docs/index.md b/docs/index.md index a7df0bc..41cf28f 100644 --- a/docs/index.md +++ b/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 diff --git a/docs/ubuntu22.system.ready.txt b/docs/ubuntu22.system.ready.txt new file mode 100644 index 0000000..aeb4439 --- /dev/null +++ b/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