Update docs: add dev_w_docker.md and include dev_w_docker.md in the d…

…ocuments

docs/dev_w_docker.md

@@ -0,0 +1,57 @@
+To develop R scripts for single cell sequencing data, docker container can be used. In the docker container, development can be finished using jupyter-lab. 
+
+If the goal is to develop an R script named `sc_singleR.prod.R`, we create two files: 
+```
+sc_seurat_opt.R
+sc_singleR.ipynb
+```
+
+1. Record the script path:
+
+```
+script_path = getwd()                                # %exclude_jupyterlab%
+script_path                                          # %exclude_jupyterlab%
+```
+
+2. Invoke `sc_singleR_opt.R` for command line options 
+
+Inside the notebook, we use the cell below to utilize `sc_seurat_opt.R` to read the command line options and save the information in an RDS file named `opt.rds`. 
+
+```
+system(paste0('Rscript ', script_path,                # %exclude_jupyterlab%
+        '/sc_singleR_opt.R --genome="hg38" --markerList="/Volumes/ccrsf-ifx/Software/scripts/bin/currentsnake/single_cell/gene_lists/human_gene_list.csv" --outdir="/Volumes/ccrsf-static/Analysis/xies4/github_repos/pipeline_dev_test/singleR" --rds="/Volumes/ccrsf-static/Analysis/xies4/github_repos/pipeline_dev_test/test_dir/seur_10x_cluster_object.rds"'),  # %exclude_jupyterlab%
+       intern = T) # %exclude_jupyterlab%
+```
+
+3. Write the main code
+
+First, read the options using readRDS: 
+
+```
+opt = readRDS("/Volumes/ccrsf-static/Analysis/xies4/github_repos/pipeline_dev_test/singleR/opt.rds")         # %exclude_jupyterlab%
+```
+
+Then include the code to accomplish the task. 
+
+4. Generate production script: `sc_singleR.prod.R`
+
+The code below will first convert the `ipynb` file to a script file and combine the script for option `sc_singleR_opt.R` and `sc_singleR.r` (output file of `jupyter nbconvert -`) with exclusion of the lines with "exclude_jupyterlab". 
+
+```
+notebook_prefix = "sc_singleR"                                                         # %exclude_jupyterlab%
+notebook_name = paste0(notebook_prefix, ".ipynb")                                     # %exclude_jupyterlab%
+notebook_r = paste0(script_path, "/", paste0(notebook_prefix, ".r"))                  # %exclude_jupyterlab%
+notebook_path = paste0(script_path, "/", notebook_name)                               # %exclude_jupyterlab%
+opt_name = paste0(script_path, "/", sub(".ipynb", "_opt.R", notebook_name))           # %exclude_jupyterlab%
+output = paste0(script_path, "/", sub(".ipynb", ".prod.R", notebook_name))            # %exclude_jupyterlab%
+cmd1 = paste0("jupyter nbconvert --to script --output ",                              # %exclude_jupyterlab%
+             notebook_prefix, ' ', notebook_path, "> /dev/null 2>&1 ")                # %exclude_jupyterlab%
+cmd1                                                                                  # %exclude_jupyterlab%
+system(cmd1, intern = TRUE)                                                            # %exclude_jupyterlab%
+cmd2 = paste0('cat ', opt_name, ' ', notebook_r,                                      # %exclude_jupyterlab%
+             ' |grep -v exclude_jupyterlab > ', output,  ' 2>&1')                     # %exclude_jupyterlab%
+cmd2                                                                                  # %exclude_jupyterlab%
+system(cmd2, intern = T)                                                              # %exclude_jupyterlab%
+system(paste0("rm ", notebook_r))                                                     # %exclude_jupyterlab%  
+```
+

mkdocs.yaml

@@ -34,7 +34,7 @@ nav:
   - Containerization for Snakemake pipeline:
       - Build Snakemake pipeline with Singularity: pipeline_containerization.md
       - Snakemake options for containerization: snakemake_opt4singularity.md 
-
+      - Develop R scripts in the container: dev_w_docker.md
   - FAQ:
       - General Questions: general-questions.md
       - Troubleshooting: troubleshooting.md