Update installation.md

docs/installation.md

@@ -1,19 +1,24 @@
 # Installation
-The package is written in the bash, so it can be used with any slurm system. To download  `scrnabox.slurm`, run the below comments 
+`scrnabox.slurm` is written in bash and can be used with any Slurm system. To download the latest version of `scrnabox.slurm` (v0.1.35) run the following command: 
 ```
-wget https://github.com/neurobioinfo/scrnabox/releases/download/v0.1.0/scrnabox.slurm.zip
-unzip scrnabox.slurm.zip 
+wget https://github.com/neurobioinfo/scrnabox/releases/download/v0.1.35/scrnabox.slurm.zip
+unzip scrnabox.slurm.zip
 ```
 
-To obtain a brief guidance of the pipeline, execute the following code.
+For a description of the options for running `scrnabox.slurm` run the following command:
 ```
 bash ./scrnabox.slurm/launch_scrnabox.sh -h 
 ```
 
-`scrnabox.slurm` needs `R` and `cellranger`. For the R, you need to install 
-`'Seurat','ggplot2', 'dplyr', 'foreach', 'doParallel', 'Matrix', 'DoubletFinder','cowplot','clustree'`. Then install `'scrnaboxR'`: 
-
+`scrnabox.slurm` requires that `R` and `cellranger` are also installed on the HPC system. In addition, the following R packages must be loaded: `'Seurat','ggplot2', 'dplyr', 'foreach', 'doParallel', 'Matrix', 'DoubletFinder','cowplot','clustree'`. Then, install the `'scrnaboxR'` R package by running the following command: 
 ```
 devtools::install_github("neurobioinfo/scrnabox/scrnaboxR")
 ```
-The `scrnaboxR` is an R package that provides a collection of functions for conducting enrichment analysis and other analyses associated with single-cell RNA sequencing (scRNA-seq) data. It serves as a companion to scrnabox, offering a range of tools and functionalities to enhance scRNA-seq data analysis. You need to add the R info in `scrnabox_config.ini`, you can define the path of R library in `R_LIB_PATH=`, version of R in `R_VERSION`, you can add the path of `cell ranger`in `MODULECELLRANGER` 
+`'scrnaboxR'` provides a collection of functions for conducting enrichment analysis and other analyses associated with scRNAseq data. It serves as a companion to scRNAbox, offering a range of tools and functionalities to enhance scRNAseq data analysis. 
+
+Please note that all R packages must be loaded into a common R library. For further instructions regarding the preparation of an R library please visit scRNAbox's [documentation](https://neurobioinfo.github.io/scrnabox/site/). Users must then define the location of their R library (`R_LIB_PATH=`), their version of R (`R_VERSION=`), and the location of CellRanger (`MODULECELLRANGER=`) in the `scrnabox_config.ini` file which is deposited into the working directory upon running the pipeline initation Step:
+```
+bash ./scrnabox.slurm/launch_scrnabox.sh \
+-d ./working_directory \
+--steps 0 \
+--method SCRNA