todays content

Author: brownsarahm

_practice/2022-10-26.md

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+1. Create an sbatch script to run your script from the review on a compute node. [see the options](https://web.uri.edu/hpc-research-computing/using-seawulf/#sbatch)
+1. **priority** File permissions are represented numerically often in octal, by transforming the permissions for each level (owner, group, all) as binary into a number. Add `octal.md` to your KWL repo and answer the following. Try to think through it on your own, but you may look up the answers, as long as you link to (or ideally cite using jupyterbook citations) a high quality source.
+    ```
+    1. Transform the permissions [`r--`, `rw-`, `rwx`] to octal, by treating it as three bits.
+    1. Transform the permission we changed our script to `rwxr-xr-x` to octal.
+    1. Which of the following would prevent a file from being edited by other people 777 or 755?
+    ```
+1. Answer the following in `hpc.md` of your KWL repo:  (to think about how the design of the system we used in class impacts programming and connect it to other ideas taught in CS)
+    ```
+    1. What kinds of things would your code need to do if you were going to run it on an HPC system?
+    1. What Sbatch options seem the most helpful?
+    1. How might you go about setting the time limits for a script? How could you estimate how long it will take?
+    ```
+1. Create `ssh.md` and include either `# 3 tips for SSH keys` or `# 3 things to avoid with SSH keys`. For each tip/misconceptions include an explanation of why it is important/wrong.  
+```{index} ssh.md
+```
+
+```{index} hpc.md
+```
+
+```{index} octal.md
+```
+
+```{admonition} Extension ideas
+1. use the server for something for another class or a side project
+1. extend your `ssh.md` file to icndlue both tips and misconceptions and/or more.
+```

_prepare/2022-10-26.md

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+1. Make sure that you have a C compiler installed on your computer. [ideally gcc](https://gcc.gnu.org/install/)
+1. Update your KWL chart. bring questions on anything we have covered so far.

_review/2022-10-26.md

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+1. Review the notes (to reinforce ideas and improve your memory of them)
+1. create a bash script that counts the number of lines in each `.fastq` file, saves the line counts to a text file, then finds how many times `Act5C` is in  `dmel-all-r6.19.gtf` on the server.  (save this on the server; we'll get it downloaded locally later)
+1. Configure ssh keys to your [GitHub account](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account) (this is actually GitHub's preferred terminal authentication method)
+1. Contribute to your group repo and review someone else's contribution

activities/practice.md

@@ -137,4 +137,11 @@ Activities:
 
 Activities:
 ```{include} ../_practice/2022-10-24.md
-```
+```
+## 2022-10-26
+
+[related notes](../notes/2022-10-26)
+
+Activities:
+```{include} ../_practice/2022-10-26.md
+```

activities/prepare.md

@@ -165,4 +165,11 @@ Activities:
 
 Activities:
 ```{include} ../_prepare/2022-10-24.md
-```
+```
+## 2022-10-26
+
+[related notes](../notes/2022-10-26)
+
+Activities:
+```{include} ../_prepare/2022-10-26.md
+```

activities/review.md

@@ -161,4 +161,11 @@ Activities:
 
 Activities:
 ```{include} ../_review/2022-10-24.md
-```
+```
+## 2022-10-26
+
+[related notes](../notes/2022-10-26)
+
+Activities:
+```{include} ../_review/2022-10-26.md
+```