tools & software rework

Author: s-sajid-ali

docs/hpc/06_tools_and_software/01_intro.md

@@ -8,8 +8,8 @@ We stongly advise that you setup your own computational enviromments via Apptain
 
 ## Package Management for R, Python, & Julia, and Conda in general
 -   [Conda environments (Python, R)](../06_tools_and_software/06_conda_environments.mdx)
--   [Using virtual environments for Python](../06_tools_and_software/02_python_packages_with_virtual_environments.mdx)
--   [Managing R packages with renv](../06_tools_and_software/03_r_packages_with_renv.mdx)
+-   [Using virtual environments for Python](../06_tools_and_software/04_python_packages_with_virtual_environments.mdx)
+-   [Managing R packages with renv](../06_tools_and_software/05_r_packages_with_renv.mdx)
 
 ## Examples of software usage on Greene 
 Examples can be found under `/scratch/work/public/examples/` and include the following

docs/hpc/06_tools_and_software/06_conda_environments.mdx

@@ -24,7 +24,7 @@ However, Conda has a significantly larger number of pre-compiled packages.
 
 ### Disadvantages
 
--   Conda does not take advantage of packages already installed in the system (while [virtualenv and venv](./02_python_packages_with_virtual_environments.mdx) do)
+-   Conda does not take advantage of packages already installed in the system (while [virtualenv and venv](./04_python_packages_with_virtual_environments.mdx) do)
 -   As you will see below, you may need to do additional steps to keep track of all installed packages (including those installed by pip and/or install.packages)
 
 ::::warning[Automatic deletion of your files]
@@ -241,7 +241,7 @@ The command `conda list --export` will not include packages installed by `instal
 
 #### `renv`
 
-Please see details of using `renv` with conda for reproducibilty on [R packages with `renv`](./03_r_packages_with_renv.mdx).
+Please see details of using `renv` with conda for reproducibilty on [R packages with `renv`](./05_r_packages_with_renv.mdx).
 
 ## Use conda env in a batch script
 The part of the batch script that will call the command should look like:

docs/hpc/06_tools_and_software/07_sqlite_handling_large_structured_data.md

@@ -79,7 +79,7 @@ conda will install pre-compiled packages. Which is good (faster) and bad (not fu
 :::
 
 :::tip
-Alternative: install packages to a local directory or use renv as described in [R Packages with renv](./03_r_packages_with_renv.mdx)
+Alternative: install packages to a local directory or use renv as described in [R Packages with renv](./05_r_packages_with_renv.mdx)
 ```sh
 mkdir /scratch/$USER/projects/myTempProject
 cd  /scratch/$USER/projects/myTempProject