added content

added quick git tutorial, quick SLURM tutorial (from google slides), server usage guidelines, updates singularity instructions, and server directory map

getting_started.md

@@ -36,7 +36,7 @@ vim ~/.config/ghostty/config
 There are *_many_* settings you can adjust in this config file, all of which you read up on in the [documentation](https://ghostty.org/docs/docs).
 
 Here's my config
-```{code}
+```{code} python
 :filename: ~/.config/ghostty/config
 :linenos:
 theme = Monokai Remastered
@@ -49,7 +49,7 @@ window-padding-balance = true
 ```
 
 #### SSH config env variable
-For ssh to work on ghostty, you need to add this to every host in your `~/.ssh/config` file which will be discussed [later](ssh_config_file)
+For ssh to work on ghostty, you need to add this to every host in your `~/.ssh/config` file which will be discussed [later](#ssh_config_file)
 ```
 SetEnv TERM=xterm-256color
 ```
@@ -121,6 +121,35 @@ mkdir -p ~/.ssh/sockets
 ```bash
 ssh [email protected]
 ```
+````{dropdown} Diectory Structure
+```mermaid
+graph TD
+    root["/"] --> boot["/boot"]
+    root --> efi["/boot/efi"]
+    root --> home["/home"]
+    root --> tank["/tank"]
+    root --> zata["/zata"]
+    
+    tank --> tank_home["/tank/home"]
+    tank_home --> dedicated["Dedicated User Mounts"]
+    
+    home --> shared_users["Regular Directory Users"]
+    home --> mounted_users["ZFS Dataset Users"]
+    
+    zata --> data["Ceph: data (4.1P)"]
+    zata --> zippy["Ceph: zippy (259T)"]
+    zata --> public["Ceph: public_html (450T)"]
+    
+    root --> tmp["/tmp"]
+    root --> run["/run tmpfs"]
+    root --> dev_shm["/dev/shm tmpfs"]
+
+    classDef network fill:#f9f,stroke:#333,stroke-width:2px
+    classDef local fill:#bbf,stroke:#333,stroke-width:2px
+    class data,zippy,public network
+    class tmp,run,dev_shm,boot,efi local
+```
+````
 
 If it's your first time, you will be prompted to scan the QR code with any two-factor authentication app. You should also be prompted to change your password. 
 ```{important}
@@ -135,6 +164,11 @@ From bastion, you can then `ssh` into any of the ZLab servers:
 ssh HOSTNAME
 ```
 
+## Server Usage Guidelines
+```{important}
+Please read the [server usage guidelines](https://docs.google.com/document/d/1X3gSpfv0avT3M3pN5HDbY3Etal_is9be-B6wJ4DJ7Fw/edit?usp=sharing) before using any of the servers.
+```
+
 # SSH
 
 ## Fixing double login issue
@@ -242,11 +276,11 @@ The remote docker image `clarity001/bioinformatics` contains a full suite of bio
 Create the destination folder and build the singularity sandbox container:
 ```bash
 mkdir -p /zata/zippy/$(whoami)/bin/
-singularity build --sandbox /zata/zippy/$(whoami)/bin/bioinformatics docker://clarity001/bioinformatics:latest
+singularity build /zata/zippy/$(whoami)/bin/bioinformatics.sif docker://clarity001/bioinformatics:latest
 ```
-To start an interactive shell in the *writable* container (optional):
+To start an interactive shell in the container (optional):
 ```bash
-singularity shell --writable -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics
+singularity shell -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics.sif
 ```
 
 (rootless_docker_setup)=
@@ -269,7 +303,7 @@ dockerd-rootless-setuptool.sh install
 ## Start a JupyterLab server using singularity
 Using the sandbox container you just built, start the JupyterLab server with the following command:
 ```bash
-singularity exec --writable -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics jupyter lab --port=8888 --ip=HOSTNAME --no-browser --notebook-dir=/data/GROUP/$(whoami)
+singularity exec -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics.sif jupyter lab --port=8888 --ip=HOSTNAME --no-browser --notebook-dir=/data/GROUP/$(whoami)
 ```
 
 ## Start a JupyterLab server in a conda environment
@@ -290,7 +324,7 @@ If you are curious, this is what the previous command is doing:
 ssh                  # The secure shell program that creates encrypted connections
 -N                   # Flag that means "don't execute a remote command/shell" - just forward ports
 -L                   # Flag for "local port forwarding"
-8888:                # The local port on your computer
+8888:                # The local port on your compute
 HOSTNAME:            # The destination server's address (check your ssh config for available hosts)
 8888                 # The remote port on the destination server
 USERNAME@HOSTNAME    # Username and server address to login to
@@ -330,11 +364,11 @@ Now start jupyter lab using your preferred method. [See Getting Started](getting
 
 Defining our config options in `jupyter_server_config.py` allows you be less declarative when starting jupyter in the terminal. For example, when using singularity we can start jupyter lab with:
 ```bash
-singularity exec --writable -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics jupyter lab
+singularity exec -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics.sif jupyter lab
 ```
 As opposed to:
 ```bash
-singularity exec --writable -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics jupyter lab --port=8888 --ip=HOSTNAME --no-browser --notebook-dir=/data/GROUP/$(whoami)
+singularity exec -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics.sif jupyter lab --port=8888 --ip=HOSTNAME --no-browser --notebook-dir=/data/GROUP/$(whoami)
 ```
 ````
 

learning_resources.md

@@ -17,51 +17,6 @@ Once you have a handle on the basics, I strongly advise moving on to learning sp
 First start with learning the basics of Linux [here](https://linuxjourney.com/). I suggest only completing the "Grasshopper" courses, as these cover most of what you need to know. After you've gotten a good grasp of the basics, then move on to learning bash scripting [here](https://exercism.org/tracks/bash). While bash scripting is useful, know when to grab for fully-featured programming language as you requirements become more complex.
 > [Bash Cheatsheet](https://devhints.io/bash)
 
-## CLI Text Editor
-Sometime you may need to quickly edit a config file or make changes to you .bashrc file. In these cases, the quickest way is almost always to use a CLI text editor. 
-
-### `vim`
-`vim` has more functionality and configurability. However, it notoriously has a steep learning curve. Here is [a good tutorial](https://github.com/iggredible/Learn-Vim/blob/master/ch00_read_this_first.md) if you are interested.
-
-### A Quick `vim` Tutorial
-
-#### Basic Navigation
-- `h/j/k/l` - Move cursor left/down/up/right 
-- `w/b` - Jump forward/backward by word
-- `0/$` - Move to start/end of line
-- `gg/G` - Go to first/last line
-
-#### Modes
-- `i` - Enter insert mode before cursor
-- `a` - Enter insert mode after cursor
-- `ESC` or `CTRL+[` - Return to normal mode
-- `v` - Enter visual mode for selection
-
-#### Essential Commands
-- `:w` - Save file
-- `:q` - Quit (`:q!` to force quit without saving)
-- `:wq` - Save and quit
-- `u` - Undo
-- `CTRL+r` - Redo
-- `dd` - Delete line
-- `yy` - Copy line
-- `p` - Paste after cursor
-
-#### Text Operations
-- `x` - Delete character
-- `dw` - Delete word
-- `cw` - Change word
-- `/pattern` - Search forward
-- `n/N` - Next/previous search result
-- `:%s/old/new/g` - Replace all occurrences
-
-You can find a more in-depth tutorial [here](https://github.com/iggredible/Learn-Vim/blob/master/ch00_read_this_first.md) if you are interested.
-
-## Version Control
-
-### Git
-The official Git documentation includes a tutorial [here](https://git-scm.com/docs/gittutorial).
-
 # Data Types and File Formats
 
 ## Sequence Data Formats