fix cellchat info and add data mngmt info

docs/devops.md

@@ -3,6 +3,25 @@
 Content ![](https://img.shields.io/badge/status-WorkInProgress-yellow)
 
 
+## Data management
+
+### AWS 
+
+- Samplesheet input files for pipelines
+    - `pipelineName_PI_hbcNNNNNN`
+    - Have a copy in project folder in O2
+    - Manually removing weekly during platform meeting
+- Raw data is under `input` folder 
+    - Alex and Lorena and Emma can move data from O2/FAS to S3
+    - `pipelineName_PI_hbcNNNNNN`
+    - lifecycle 14 days
+- Pipeline outputs are under `results`:
+    - `pipelineName_PI_hbcNNNNNN`
+    - lifecycle 14 days for bigger than 1gb
+    - Move output pipeline to project folder under `final` folder
+- Data cleaning every platform meeting
+- Quarterly Evaluation: RNAseq, CHIPseq
+
 ## Configure to use posit package manager
 
 [source](https://packagemanager.posit.co/client/#/repos/bioconductor/setup?bioconductor_version=3.18)
@@ -20,23 +39,29 @@ options(repos = c(CRAN = "https://packagemanager.posit.co/cran/2024-05-01"))
 
 ### CELLCHAT
 
-```
-module load  miniconda3/23.1.0
+Add `python/3.9.14` to the modules load to Rstudio in O2 ondemand.
 
-conda create -p /n/app/bcbio/R4.3.1_python -c conda-forge umap-learn
+```
+# To install python deps
+virtualenv_install("/n/app/bcbio/R4.3.1_python_cellchat", packages="umap-learn==0.5.5",python_version="3.9",force=TRUE)
+virtualenv_install("/n/app/bcbio/R4.3.1_python_cellchat", packages="numpy==1.26",python_version="3.9")
+#.rs.restartR() # restart R manually if outside RStudio
+reticulate::py_config() # check it is pointing to right versions: umap-learn 0.5.5 and umap 1.26
+Sys.getenv("PYTHONPATH") # needs to be empty
 
+# R package
 BiocManager::install("BiocNeighbors")
 install.packages('NMF')
 install.packages("circlize")
 devtools::install_github("jinworks/CellChat")
 
-library(reticulate)
-# create a new environment 
-virtualenv_create("/n/app/bcbio/R4.3.1_python_sc_20240522snapshot")
-# install umap
-virtualenv_install("/n/app/bcbio/R4.3.1_python_sc_20240522snapshot", "umap-learn")
-# indicate that we want to use a specific virtualenv
-use_virtualenv("/n/app/bcbio/R4.3.1_python_sc_20240522snapshot")
+
+# To use it
+reticulate::use_virtualenv("/n/app/bcbio/R4.3.1_python_cellchat")
+reticulate::py_config() # check it is pointing to right versions: umap-learn 0.5.5 and umap 1.26
+Sys.getenv("PYTHONPATH") # needs to be empty
+
 py_module_available(module = 'umap')
 reticulate::import(module = "umap", delay_load = TRUE)
+library(CellChat)
 ```