finish 1st draft of part 2 slides

2025-11-30 09:45:43 -08:00 · 2024-03-27 13:14:21 -07:00 · 2024-03-27 13:14:21 -07:00 · 2520c89e03
commit 2520c89e03
parent 7be6cc5b90
7 changed files with 2028 additions and 98 deletions
--- a/docs/Working_on_Wynton_Part_1.html
+++ b/docs/Working_on_Wynton_Part_1.html
--- a/docs/Working_on_Wynton_Part_2.html
+++ b/docs/Working_on_Wynton_Part_2.html
--- a/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
+++ b/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
@ -16,7 +16,7 @@ output:
 ---

 ```{r, setup, include=FALSE}
-library(tidyverse)
+
 ```

 ## 
@ -28,7 +28,7 @@ library(tidyverse)
 **Natalie Elphick**    
 Bioinformatician I   

-**Alex Pico (TA)**     
+**Alex Pico**     
 Bioinformatics Core Director


@ -61,6 +61,7 @@ Bioinformatics Core Director
 ## Wynton {.small-bullets}

 -   A HPC Linux environment available to all UCSF researchers for free   
+-   Uses the Rocky 8 linux OS
 -   Includes several hundred compute nodes and a large shared storage system ([Cluster specifications](https://wynton.ucsf.edu/hpc/about/specs.html))    
 -   Funded and administered cooperatively by UCSF campus IT and key research groups   

@ -136,11 +137,36 @@ echo "{local}$ scp local_file.tsv alice@dt1.wynton.ucsf.edu:~/"
 dt1 and dt2


+
+## Compute Nodes {.small-bullets .big-picture}
+
+-   Can **not** be logged in to directly
+-   Used to run non-interactive compute job scripts
+-   The software to run the job script is provided using a container
+
+
+![Compute Jobs](slide_materials/compute_job_workflow.svg)
+
+
+
 # Storage

+
+## The File System {.small-bullets}
+
+-   A file system how information is stored and retrieved on a computer
+      -   Consists of files and directories
+-   A local file system is function of the operating system and only accessible from a single computer
+-   A shared file system is accessible from multiple computers
+
+
+
+
+
+
 ## BeeGFS {.small-bullets}

-   Wynton uses a *parallel* file system called BeeGFS
+-   Wynton uses a *parallel* shared file system called BeeGFS
    - The files are stored as "chunks" spread across many different servers
 -   BeeGFS has multiple services that work together to manage the file system
    - Storage (stores the chunks)
@ -162,12 +188,11 @@ dt1 and dt2
 ## BeeGFS - I/O patterns {.small-bullets}
 -   Anything that requires lots of metadata operations can feel slow 
    -   e.g: lots of writes to the same directory and lots of file lookups and directory searches (**conda**)
-   Users are strongly encouraged to keep the number of reads and writes to a single directory to a reasonable number
-   If using conda, putting the conda application inside a Apptainer (formerly singularity) container will result in better overall file system performance
+-   Keep the number of reads and writes to a single directory to a reasonable number
+-   If using conda, putting the conda application inside a Apptainer (formerly singularity) container will result in better performance

 ## BeeGFS - Tips 

-   Some general guidelines for optimum use of BeeGFS
 -   Prefer fewer, large files over many small ones
 -   Distribute reading and writing over several directories
    -   Including compute job output and error files
@ -184,6 +209,7 @@ dt1 and dt2
    - User home directory - limited to 500 GiB
 -   /wynton/**[group_name]**
    - User group directory - disk quota varies by group
+    - Use this directory for any analysis you want to share with your lab
 -   [More information on disk quotas](https://wynton.ucsf.edu/hpc/howto/storage-size.html#file-sizes-and-disk-quotas)

 To check your group disk quota run:
@ -211,13 +237,22 @@ echo 'beegfs-ctl --getquota --storagepoolid=12 --gid "$(id --group)"'
 -   Gladstone's HIVE storage server is mounted directly to Wynton under **/gladstone**
    -   Only certain HIVE folders are accessible directly on Wynton
    -   Files under **/gladstone** are backed up
-   Naming: **/gladstone/[lab]/[share]**
+-   Naming: **/gladstone/[lab]**
+    -   Directories that are shared between multiple labs can be set up by contacting Gladstone IT   
 -   For more information visit the [IT knowledge base page](https://help.gladstone.org/support/solutions/articles/14000033963)


+## Storage Advice
+
+-   Always back up anything you store under **/wynton**
+-   Use **/gladstone** if you have access to it for all of your work since it is automatically backed up
+-   Use the scratch directories to store temporary files so they do not count against your group or user quotas
+

 # Data Transfer

+
+
 ## Secure Copy - scp

 -   Local file to Wynton
@ -252,7 +287,7 @@ echo "{local}$ scp alice@dt1.wynton.ucsf.edu:/path/to/local_file.tsv /destinatio

 ## Globus

-   [Globus](https://wynton.ucsf.edu/hpc/transfers/globus.html) is a non-profit service for moving, syncing, and sharing large amounts of data asynchronously in the background
+-   [Globus](https://wynton.ucsf.edu/hpc/transfers/globus.html) is a service for moving, syncing, and sharing large amounts of data
 -   Wynton Accounts are not required to transfer data with Globus
 -   Useful for transferring data between institutions

@ -264,12 +299,33 @@ echo "{local}$ scp alice@dt1.wynton.ucsf.edu:/path/to/local_file.tsv /destinatio
 -   Do not use rclone for transfers to Box, follow the [Wynton to UCSF Box](https://wynton.ucsf.edu/hpc/transfers/ucsf-box.html) instructions


+
+
+## Poll 1 
+
+Which of these can you **not** log in to from your computer?
+
+1.    Login Nodes
+2.    Development Nodes
+3.    Data transfer Nodes
+4.    Compute Nodes
+
+## Poll 2
+
+The **/wynton** directory is backed up on a nightly basis so do not need to back up the data you store here.
+
+1.    True
+2.    False
+
+
+
+
 # Installing Software

 ## Basics

-   Ensure the software you are trying to install is compatible with Rocky linux (use a container if not)
-   Check if the tool is already available in a [module](https://wynton.ucsf.edu/hpc/software/software-modules.html)
+-   Check if the tool is already available in a [module](https://wynton.ucsf.edu/hpc/software/software-repositories.html#software-repositories)
+-   Ensure the software you are trying to install is compatible with Rocky 8 linux (use a container if not)
 -   <u>Always install software in a development node</u>
 -   Download a precompiled binary or [install from source](https://wynton.ucsf.edu/hpc/howto/install-from-source.html)

@ -297,10 +353,12 @@ echo '[alice@dev1 ~]$ make'
 echo '[alice@dev1 ~]$ make install'
 ```

-## Install Nextflow for Part 2
+## Install Nextflow
+
+-   Scientific workflow system with a community maintained set of [core bioinformatics analysis](https://nf-co.re/) pipelines
+    -   We will cover an example RNA-seq pipeline in part 2   
+-   These can be configured to use the Wynton compute job submission system 

-   In part 2, we will run the nextflow rna-seq pipeline
-   Run the following to install nextflow:

 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo '[alice@dev1 ~]$ cd ~/software'
@ -312,16 +370,25 @@ echo '[alice@dev1 ~]$ wget -qO- https://get.nextflow.io | bash'
 ```


- Let us know if you run into any errors
+


 # Containers

+
+## Motivation {.small-bullets}
+
+-   Compute heavy jobs (high RAM, multiple cores) should be run on compute nodes
+-   Containers allow us to make additional software available to the compute nodes
+    -   Also allows the use of software that might be hard to install on Rocky 8 Linux
+    -   Improves reproducibility
+
+![Compute Jobs](slide_materials/compute_job_workflow.svg)
+
+
 ## Definitions {.small-bullets}

 -   **Virtualization:** When software mimics the functions of physical hardware to run virtual machines
-    -   Work around to use OS specific or legacy software that might be hard to install
-    -   Improves reproducibility
 -   **Containers:** Implements virtualization using an *image* as its base
 -   **Images:**  An ordered collection of root filesystem changes and the corresponding execution parameters for use within a container runtime

@ -329,7 +396,7 @@ echo '[alice@dev1 ~]$ wget -qO- https://get.nextflow.io | bash'
 ## Apptainer {.small-bullets}

 -   Wynton supports [Apptainer](https://wynton.ucsf.edu/hpc/software/apptainer.html) (formerly singularity) containers 
-   [Docker](https://docs.docker.com/) is a commonly used container creation software, these can be turned into apptainer containers easily
+-   [Docker](https://docs.docker.com/) is a commonly used image creation software, these can be turned into apptainer image files (.sif) easily

 -   apptainer run <image_file>
    -   Run predefined script within container
@ -362,7 +429,7 @@ echo '    __  __     ____         _       __           __    __   __
 ```


-## Example Container - Hello World
+## Example Container

 -   This container has **figlet** installed which creates ASCII art from text input
 -   Try running this command to create your own using *exec*
@ -376,7 +443,8 @@ echo '[alice@dev1 ~]$ apptainer exec hello-world_1.0.sif figlet your_text'
 -   Docker uses Dockerfiles to specify image creation
 -   Preferred by the Gladstone Bioinformatics Core to create new images
 -   In part 2, we will go over how to build custom container images from DockerFiles
-    - If you want to follow along, [install the docker engine](https://docs.docker.com/engine/install/) following the instructions for your OS
+    -   If you want to follow along, [install the docker engine](https://docs.docker.com/engine/install/) following the instructions for your OS
+    -   Set up a free [DockerHub](https://hub.docker.com/) account to store your images
 -   To see the Dockerfile used to create the hello-world image, run:

 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
@ -405,8 +473,6 @@ April 29-April 30, 2024 9am-4pm PDT
 May 6-May 7, 2024 1-4pm PDT


-
-[Complete Schedule](https://gladstone.org/events)     
-Click "Data Science Training Program"
+[Complete Schedule](https://gladstone.org/events?series=189)     


--- a/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd
+++ b/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd
@ -0,0 +1,449 @@
+---
+title: "Working on Wynton - Part 2"
+author: "Natalie Elphick"
+date: "April 16th, 2024"
+knit: (function(input, ...) {
+    rmarkdown::render(
+      input,
+      output_dir = "../docs"
+    )
+  })
+output:
+  revealjs::revealjs_presentation:
+    theme: simple
+    highlight: default
+    css: style.css
+---
+
+```{r, setup, include=FALSE}
+
+```
+
+## 
+
+<center>*Press the ? key for tips on navigating these slides*</center>
+
+## Introductions
+
+**Natalie Elphick**    
+Bioinformatician I   
+
+**Alex Pico**     
+Bioinformatics Core Director
+
+
+## Target Audience
+-   Prior experience with UNIX command-line 
+
+
+
+## Part 2:
+
+1.    Custom Containers
+2.    Submitting Compute Jobs
+3.    Array Jobs
+4.    GPU Jobs
+5.    Running Pipelines
+6.    Jupyter Notebooks 
+7.    RStudio Server
+8.    How to get help
+
+
+
+
+# Custom Containers
+
+## Motivation {.small-bullets}
+
+-   Compute heavy jobs (high RAM, multiple cores) should be run on compute nodes
+-   Containers allow us to make additional software available to the compute nodes
+    -   Also allows the use of software that might be hard to install on Rocky 8 Linux
+    -   Improves reproducibility
+
+![Compute Jobs](slide_materials/compute_job_workflow.svg)
+
+
+
+
+## Dockerfile Basics
+
+-   Dockerfiles contain instructions to build an image in **layers**
+-   Layers are added using Dockerfile instruction syntax
+-   Images are built by navigating to the directory that contains the Dockerfile and running:
+
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo 'docker build .'
+```
+
+## Dockerfile Instructions {.small-bullets}
+-   First instruction is always **FROM** which specifies the base image
+    -   Base images are a starting point with some basics already installed like the OS and build tools, find them on [DockerHub](https://hub.docker.com/)
+-   **RUN** : Use before running any shell commands
+-   **SHELL** : Set the shell
+-   **USER** : Set the user (within the image)
+-   **CMD** : Set the default instruction to be run by the image
+-   **COPY** : COPY files into the image
+
+
+See the [Dockerfile documentation](https://docs.docker.com/reference/dockerfile/) for a full list of instructions
+
+## Example Dockerfile {.code-alt}
+
+-   Click [here](https://www.dropbox.com/scl/fi/mdbefp3h8ahdvxtgjypqo/Dockerfile?rlkey=7d4zd9ge1m3wwszlfy78712ky&dl=1) to download the example Dockerfile
+-   Open in your preffered text editor
+
+
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+curl -s -L -o Dockerfile 'https://www.dropbox.com/scl/fi/mdbefp3h8ahdvxtgjypqo/Dockerfile?rlkey=7d4zd9ge1m3wwszlfy78712ky&dl=0'
+cat Dockerfile
+rm Dockerfile
+```
+
+## Building Example Image
+
+-   Do not run this during the workshop
+    -   It requires a lot of RAM
+-   On macOS, make sure you have the Docker Desktop App running
+-   We can provide an additional argument to the **build** command, -t, to set the name of the docker image
+      -   We can add version tags after the name using ":" 
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo "docker build -t docker_hub_user/seurat-harmony:1.0 ."
+```
+
+
+## Pushing Images to DockerHub  {.small-bullets}
+
+-   Make sure you are signed in to your DockerHub account locally (Docker Desktop for macOS)
+-   The image name must start with your user name
+
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo "docker push docker_hub_user/seurat-harmony:1.0"
+```
+
+-   These can then be "pulled" on to Wynton as apptainer image files (image must be public)
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo "[alice@dev1 ~]$ apptainer pull docker://docker_hub_user/seurat-harmony:1.0"
+```
+
+## Notes on Building Custom Images {.code-small}
+
+-   Time consuming process and uses a lot of RAM on your local machine
+-   A good base image can save you a lot of time
+-   You must run `apt-get update` and `apt-get install` in the same command
+    -   Otherwise you will encounter caching issues
+-   Remember to use `apt-get install -y`
+    -   You will have no control over the process while it's building
+
+# Compute Jobs
+
+
+## Submission Script - Basics {.small-bullets .code-alt}
+
+-   [Download](https://www.dropbox.com/scl/fi/fzp33y1ojslw005q8epuz/simple_submission_script.sh?rlkey=xmg3lqec962y3i57a1bkriosx&dl=1) this example job submission script
+-   Read the full Wynton [job submission guide](https://wynton.ucsf.edu/hpc/scheduler/submit-jobs.html)
+-   Wynton uses the [Sun Grid Engine](https://web.archive.org/web/20210826212738/https://arc.liv.ac.uk/SGE/howto/howto.html) job scheduler
+
+
+
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+curl -s -L -o submission.sh 'https://www.dropbox.com/scl/fi/fzp33y1ojslw005q8epuz/simple_submission_script.sh?rlkey=xmg3lqec962y3i57a1bkriosx&dl=0'
+cat submission.sh
+rm submission.sh
+```
+
+## Submission Script - Apptainer {.small-bullets .code-alt}
+
+-   [Download](https://www.dropbox.com/scl/fi/zzl9fnfcoxu3pyrx5ffd1/apptainer_submission_script.sh?rlkey=w05e18ahw4hvbvaucac379za9&dl=1) this example job submission script that uses a container
+-   Paths that the container needs read/write access to need to be mounted with APPTAINER_BINDPATH
+
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+curl -s -L -o submission.sh 'https://www.dropbox.com/scl/fi/zzl9fnfcoxu3pyrx5ffd1/apptainer_submission_script.sh?rlkey=w05e18ahw4hvbvaucac379za9&dl=1'
+cat submission.sh
+rm submission.sh
+```
+
+## Parallel Processing Jobs {.small-bullets}
+
+-   By default jobs run on a single core
+-   Multicore jobs must run in a SGE parallel environment (PE) and tell SGE how many cores the job will use
+-   **Do not use more cores than requested**
+
+
+-   There are four parallel environments on Wynton:
+    -   **smp**: for single-host parallel jobs using [Symmetric multiprocessing](https://en.wikipedia.org/wiki/Symmetric_multiprocessing) (SMP)
+    -   **mpi**: for multiple-host parallel jobs based on [MPI parallelization](https://en.wikipedia.org/wiki/Message_Passing_Interface)
+    -   **mpi_onehost**: for single-host parallel jobs based on MPI parallelization
+    -   **mpi-8**: for multi-threaded multi-host jobs based on MPI parallelization
+
+## Example Parallel Job {.small-bullets .code-alt}
+
+-   The simplest parallel environment on Wynton is **smp**, a single node with *n* cores
+-   [Download](https://www.dropbox.com/scl/fi/71xo0cioh266pj3uwcdps/smp_submission_script.sh?rlkey=kw7qaz8pip6jveqv317b5swqr&dl=1) this example smp job submission script
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+curl -s -L -o submission.sh 'https://www.dropbox.com/scl/fi/71xo0cioh266pj3uwcdps/smp_submission_script.sh?rlkey=kw7qaz8pip6jveqv317b5swqr&dl=0'
+cat submission.sh
+rm submission.sh
+```
+
+
+## Array Jobs {.small-bullets .code-alt}
+
+-   This is a good option if the script you want to run operates on discrete sets of data
+    - e.g. sample or chromosome
+-   [Download](https://www.dropbox.com/scl/fi/upl71jeny62fxfzkxao1f/array_job_submission_script.sh?rlkey=ggkyjxx8nz400e1t96mif5t34&dl=1) this example array job submission script
+
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+curl -s -L -o submission.sh 'https://www.dropbox.com/scl/fi/upl71jeny62fxfzkxao1f/array_job_submission_script.sh?rlkey=ggkyjxx8nz400e1t96mif5t34&dl=0'
+cat submission.sh
+rm submission.sh
+```
+
+## GPU Jobs  {.small-bullets}
+
+-   To run a [GPU job](https://wynton.ucsf.edu/hpc/scheduler/gpu.html), specify **-q gpu.q** (queue) as a GPU queue
+    -   Other GPU queues may be available to you depending on your lab
+-   It is important to specify the GPU using the **SGE_GPU** variable so that your job uses its assigned GPU
+    -   For CUDA based tools, add **export CUDA_VISIBLE_DEVICES=$SGE_GPU** to your submission script
+-   GPU jobs must include a runtime request or they will be removed from the queue
+
+
+## Submitting and Querying jobs
+
+-   Use **qsub** to submit jobs
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo '[alice@dev1 ~]$ qsub job1.sh
+Your job 714888 ("job1.sh") has been submitted'
+```
+
+
+
+
+-   Use **qstat** to check the status of your jobs
+
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo '[alice@dev1 ~]$ qstat
+job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
+-----------------------------------------------------------------------------------------------------------------
+ 714888 0.06532 job1 alice     r     03/25/2024 19:54:18 member.q@msg-hmio1                 1        
+ 714889 0.06532 job2 alice     r     03/25/2024 19:54:19 member.q@msg-hmio1                 1        
+'
+```
+
+
+Read the [querying jobs](https://wynton.ucsf.edu/hpc/scheduler/list-jobs.html) Wynton documentation for more information.
+
+
+## Estimating Job Resources
+
+-   Try to estimate the amount of RAM needed using a small test dataset
+-   Request a little more RAM than you need to avoid having your job cancelled
+-   Check on jobs you are running for the first time with **qstat -j <job-id>** to make sure they are not going over
+
+
+## Poll 3
+
+Anything that you can run on a compute node can be run on a development node.
+
+1.    True
+2.    False
+
+
+
+# Running Pipelines
+
+
+## Nextflow RNA-seq {.small-bullets .big-picture}
+
+-   Scientific workflow system with a community maintained set of core bioinformatics [analysis pipelines](https://nf-co.re/)
+-   The most commonly used one is the [RNA-seq pipeline](https://nf-co.re/rnaseq/3.14.0)
+
+![RNA-seq](slide_materials/nf-core-rnaseq_metro_map_grey.png)
+
+
+## Example - RNA-seq Pipeline {.small-bullets}
+
+**Do not run this during the workshop as it will fill up the Wynton SGE queue**
+
+-   Download the [testing script](https://www.dropbox.com/scl/fi/3c9qdmnwg8vw9x517mo05/nextflow_example.sh?rlkey=e9nxbvpcdtdyi5w0y16z9k7bq&dl=0)
+    -   Runs a minimal test on the RNA-seq pipeline
+-   Download the [config file](https://www.dropbox.com/scl/fi/befhl3z6nipn1fqcxpqth/nextflow.config?rlkey=pd8d9vup6pnvb7bbrmekayn2j&dl=0)
+    -   Configures nextflow to use the SGE job scheduler and sets limits on compute job resources for each process
+-   Put these in the same directory (do not use your user home directory for this) and run the script in a screen/tmux session
+-   When not running the test, the **-profile** should be apptainer
+
+
+
+
+
+
+
+# Jupyter Notebooks 
+
+## Installing Jupyter Notebooks
+-   The preferred way to install and use [Jupyter notebooks](https://wynton.ucsf.edu/hpc/howto/jupyter.html) on Wynton is though pip, not conda
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo 'python3 -m pip install --user notebook'
+```
+-   Jupyter notebooks can only be run on development nodes
+-   See the Wynton [python documentation](https://wynton.ucsf.edu/hpc/howto/python.html) for more info on managing python environments on Wynton
+
+
+## Running Jupyter Notebooks - Step 1
+
+-   You cannot connect from outside Wynton HPC directly to a development node
+    -   Instead we need to use SSH port forwarding to establish the connection with a local web browser
+-   Find an available TCP port:
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo '[alice@dev1 ~]$ module load CBI port4me
+[alice@dev1 ~]$ port4me --tool=jupyter
+47467'
+```
+
+Note the port number returned by port4me, you will need this later.
+
+
+## Running Jupyter Notebooks - Step 2 {.code-small}
+-   Launch Jupyter notebook using the port numer from step 1
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo '[alice@dev1]$ jupyter notebook --no-browser --port 47467
+[I 2024-03-20 14:48:45.693 ServerApp] jupyter_lsp | extension was successfully linked.
+[I 2024-03-20 14:48:45.698 ServerApp] jupyter_server_terminals | extension was successfully linked.
+[I 2024-03-20 14:48:45.703 ServerApp] jupyterlab | extension was successfully linked.
+[I 2024-03-20 14:48:45.708 ServerApp] notebook | extension was successfully linked.
+[I 2024-03-20 14:48:46.577 ServerApp] notebook_shim | extension was successfully linked.
+[I 2024-03-20 14:48:46.666 ServerApp] notebook_shim | extension was successfully loaded.
+[I 2024-03-20 14:48:46.668 ServerApp] jupyter_lsp | extension was successfully loaded.
+[I 2024-03-20 14:48:46.669 ServerApp] jupyter_server_terminals | extension was successfully loaded.
+[I 2024-03-20 14:48:46.675 LabApp] JupyterLab extension loaded from /wynton/home/boblab/alice/.local/lib/python3.11/site-packages/jupyterlab
+[I 2024-03-20 14:48:46.675 LabApp] JupyterLab application directory is /wynton/home/boblab/alice/.local/share/jupyter/lab
+[I 2024-03-20 14:48:46.677 LabApp] Extension Manager is 'pypi'.
+[I 2024-03-20 14:48:46.707 ServerApp] jupyterlab | extension was successfully loaded.
+[I 2024-03-20 14:48:46.711 ServerApp] notebook | extension was successfully loaded.
+[I 2024-03-20 14:48:46.712 ServerApp] Serving notebooks from local directory: /wynton/home/boblab/alice
+[I 2024-03-20 14:48:46.712 ServerApp] Jupyter Server 2.13.0 is running at:
+[I 2024-03-20 14:48:46.712 ServerApp] http://localhost:44214/tree?token=8e37f8d62fca6a1c9b2da429f27df5ebcec706a808c3a8f2
+[I 2024-03-20 14:48:46.712 ServerApp]     http://127.0.0.1:44214/tree?token=8e37f8d62fca6a1c9b2da429f27df5ebcec706a808c3a8f2
+[I 2024-03-20 14:48:46.712 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
+[C 2024-03-20 14:48:46.725 ServerApp]
+
+    To access the server, open this file in a browser:
+        file:///wynton/home/boblab/alice/.local/share/jupyter/runtime/jpserver-2853162-open.html
+    Or copy and paste one of these URLs:
+        http://localhost:44214/tree?token=8e37f8d62fca6a1c9b2da429f27df5ebcec706a808c3a8f2
+        http://127.0.0.1:44214/tree?token=8e37f8d62fca6a1c9b2da429f27df5ebcec706a808c3a8f2'
+```
+
+## Running Jupyter Notebooks - Step 3
+
+- Set up SSH port forwarding on your local machine in a separate terminal, leave both terminals open
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo '{local}$ ssh -J alice@log1.wynton.ucsf.edu -L 47467:localhost:47467 alice@dev1
+...
+[alice@dev1 ~]$ '
+```
+
+The notebook should now be available at the URL from step 2
+
+
+# RStudio Server
+
+## RStudio Server
+-   [RStudio server](https://wynton.ucsf.edu/hpc/howto/rstudio.html) is already available in the CBI module
+-   This allows you to set up a personal RStudio instance that only you can access
+-   Requires two separate SSH connections to the cluster:\
+    -   One to launch RStudio Server
+    -   One to connect to it
+
+
+## RStudio Server - Step 1 {.code-small}
+
+-   Launch your own RStudio Server instance
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo '[alice@dev1 ~]$ module load CBI rstudio-server-controller
+[alice@dev1 ~]$ rsc start
+alice, your personal RStudio Server 2023.09.1-494 running R 4.3.2 is available on:
+
+  <http://127.0.0.1:20612>
+
+Importantly, if you are running from a remote machine without direct access
+to dev1, you need to set up SSH port forwarding first, which you can do by
+running:
+
+  ssh -L 20612:dev1:20612 alice@log1.wynton.ucsf.edu
+
+in a second terminal from your local computer.
+
+Any R session started times out after being idle for 120 minutes.
+WARNING: You now have 10 minutes, until 2023-11-15 17:06:50-08:00, to
+connect and log in to the RStudio Server before everything times out.
+Your one-time random password for RStudio Server is: y+IWo7rfl7Z7MRCPI3Z4'
+```
+
+Note the password and URL, they will be needed to log in to the server instance.
+
+
+## RStudio Server - Step 2
+
+-   Connect to your personal RStudio Server instance from your local machine in a separate terminal
+```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
+echo '{local}$ ssh -L 20612:dev1:20612 alice@log1.wynton.ucsf.edu
+alice1@log1.wynton.ucsf.edu:s password: XXXXXXXXXXXXXXXXXXX
+[alice@log1 ~]$ '
+```
+
+## RStudio Server - Step 3
+-   Open RStudio Server in your local web browser
+-   Open the link from step 1
+-   Enter your Wynton user name
+-   Enter the password from step 1
+
+# How to Get Help
+
+## Wynton Questions
+
+-   Follow the Wynton [question checklist](https://wynton.ucsf.edu/hpc/support/index.html)
+-   Email
+    -   [support@wynton.ucsf.edu](mailto:support@wynton.ucsf.edu)
+-   Slack
+    -   [ucsf-wynton](https://join.slack.com/t/ucsf-wynton/signup)
+    -   Sign-up using a UCSF email address
+    -   Email support if that does not work
+-   Zoom office hours every **Tuesday at 11-12pm**
+    -   Zoom URL in the message-of-the-day (MOTD) that you get when you log into Wynton
+
+
+
+## Bioinformatics Questions
+
+-   Email
+    -   [bioinformatics@gladstone.ucsf.edu](mailto:bioinformatics@gladstone.ucsf.edu)
+-   Slack channel #questions-about-bioinformatics
+    -   Contact us at the email above to be added to the channel
+
+
+
+# End of Part 2
+
+## Thank You!
+
+-   Please take some time to fill out the workshop survey:   
+[https://www.surveymonkey.com/r/F75J6VZ](https://www.surveymonkey.com/r/F75J6VZ)
+
+
+## Upcoming Data Science Training Program Workshops
+
+
+[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models)   
+April 25-April 26, 2024 1-3pm PDT
+
+[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis)     
+April 29-April 30, 2024 9am-4pm PDT
+
+[Single Cell ATAC-Seq Data Analysis Part 1](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-1-1)    
+May 6-May 7, 2024 1-4pm PDT
+
+
+[Complete Schedule](https://gladstone.org/events?series=189)     
+
+
+
--- a/working-on-wynton-hpc/slide_materials/compute_job_workflow.svg
+++ b/working-on-wynton-hpc/slide_materials/compute_job_workflow.svg
--- a/working-on-wynton-hpc/slide_materials/nf-core-rnaseq_metro_map_grey.png
+++ b/working-on-wynton-hpc/slide_materials/nf-core-rnaseq_metro_map_grey.png
--- a/working-on-wynton-hpc/style.css
+++ b/working-on-wynton-hpc/style.css
@ -12,17 +12,21 @@

 .reveal code {
    background-color: #1e1e1eef; /* Dark background for code chunks */
-    color: white !important; /* White text for code */
+    color: white; /* White text for code */
    font-size: 1.2em;
    line-height: 1.2;
 }

-.reveal code::selection {
-    background-color: #d97306 !important; /* Dark magenta background for selected text */
+.code-small code {
+    background-color: #1e1e1eef; /* Dark background for code chunks */
+    color: white; /* White text for code */
+    font-size: 1em;
+    line-height: 1;
 }

-
-
+.reveal code::selection {
+    background-color: #d97306 !important; /* Dark orange background for selected text */
+}


 /* Specific styles for code output: background */
@ -30,11 +34,17 @@
    background-color: black; /* Black background for code outputs */
 }

-/* Style for text selection within code outputs */
-.reveal pre code.output::selection {
-    background-color: #9c0366 !important; /* Dark magenta background for selected text in outputs */
+/* Custom class for code alt display */
+.code-alt code {
+    background-color: #ffecd0ac; /* Dark background for code outputs */
+    max-height: 400px !important;
+    font-family: 'Menlo', sans-serif;
+    font-size: 0.8em;
+    color: rgb(76, 76, 76)
 }

+
+
 /* Code output text color */
 .reveal pre code.output {
    color: white;
@ -63,32 +73,34 @@ pre, code, kbd, samp {
    white-space: pre !important;
    overflow-x: auto !important;
 }
+
+/* Change the font family used for all text except code */
+.reveal p, .reveal li, .reveal h1, .reveal h2, .reveal h3, .reveal h4, .reveal h5, .reveal h6 {
+    font-family: "Helvetica", sans-serif;
+}
+
+.reveal h3 {
+    color: black;
+    font-size: 0.7em;
+}
 /* Bold slide titles and change color */
 .reveal h2 {
    font-weight: bold !important;
    color: #9c0366;
+    font-size: 1.3em;
 }
 /* Bold slide titles and change color */
 .reveal h1 {
    font-weight: bold !important;
    color: #9c0366;
+    font-size: 2.0em;
 }
+
 .reveal .slides>section:first-child h2 {
-    color: #333;
+    color: black;
    font-weight: normal !important;
-  }
-/* Custom slide title */
-.my-title-slide h1 {
-    font-weight: bold;
-    color: #9c0366;
-  }
-.my-title-slide h2 {
-color: #333;
-font-weight: normal !important;
 }

-
-
 .reveal .slides>section:first-child h1 {
    font-weight: bold !important;
    color: #9c0366;
@ -107,12 +119,13 @@ font-weight: normal !important;

 .reveal ul ul {
    font-size: 0.75em; /* Smaller font size */
-    margin-top: 5px !important;
    margin-bottom: 5px !important;
 }
 .reveal ol {
    display: block;
-    margin-bottom: 20px !important;
+    margin-bottom: 20px;
+    margin-left: 75px;
+    margin-right: 50px
 } 


@ -147,16 +160,16 @@ small {
 }

 .big-picture img{
-    max-width: 70%;
-    border: 1px solid black !important;
+    max-width: 95%;
+
 }

-/* Chage link color to purple */
+/* Chage link color to sky blue */
 .reveal a {
-    color: #0c74dc !important;
+    color: #0c74dc;
 }

-/* Change link color to purple on hover */
+/* Change link color to magenta on hover */
 .reveal a:hover {
    color: #9c0366 !important;
 }