fixed broken links

Author: RobJY

docs/hpc/06_tools_and_software/01_software_on_greene.md

@@ -7,7 +7,7 @@ There are different types of software packages available
     -   This includes the licensed software listed below
 -   Singularity Containers
     -   You can find those already built and ready to use, at location `/scratch/work/public/singularity/`
-    -   For more information on running software with Singularity, See [Singularity: Run Custom Applications with Containers](../07_containers/05_singularity_run_custom_applications_with_containers.md).
+    -   For more information on running software with Singularity, See our [Containers Intro](../07_containers/01_intro.md).
 -   Python/R/Julia packages can be installed by a user 
 
 If you need another linux program installed, please contact us at [hpc@nyu.edu](mailto:hpc@nyu.edu) 
@@ -32,9 +32,9 @@ Below is a list of modules and their associated functions:
 
 
 ## Package Management for R, Python, & Julia, and Conda in general
--   [Conda environments (Python, R)](../06_tools_and_software/02_conda_environments.md)
--   [Using virtual environments for Python](../06_tools_and_software/03_python_packages_with_virtual_environments.md)
--   [Managing R packages with renv](../06_tools_and_software/04_r_packages_with_renv.md)
+-   [Conda environments (Python, R)](../06_tools_and_software/04_conda_environments.md)
+-   [Using virtual environments for Python](../06_tools_and_software/02_python_packages_with_virtual_environments.md)
+-   [Managing R packages with renv](../06_tools_and_software/03_r_packages_with_renv.md)
 
 ## Examples of software usage on Greene 
 Examples can be found under `/scratch/work/public/examples/` and include the following

docs/hpc/07_containers/03_singularity_with_conda.md

@@ -287,7 +287,7 @@ pip install tensorboard
 ```
 
 :::note
-[Click here](../06_tools_and_software/02_conda_environments.md) for information on how to configure your conda environment.
+[Click here](../06_tools_and_software/04_conda_environments.md) for information on how to configure your conda environment.
 :::
 
 Please also keep in mind that once the overlay image is opened in default read-write mode, the file will be locked. You will not be able to open it from a new process. Once the overlay is opened either in read-write or read-only mode, it cannot be opened in RW mode from other processes either. For production jobs to run, the overlay image should be open in read-only mode. You can run many jobs at the same time as long as they are run in read-only mode. In this ways, it will protect the computation software environment, software packages are not allowed to change when there are jobs running.