tgen/Institutional_Instructions

Description of institutional rules and regulations regarding the usage of github, plus usage guidelines

Institutional Instructions

Description of institutional rules and regulations regarding the usage of github, plus usage guidelines

1. All code should be stored in github to allow institutional sharing and proper version control
2. All new repositories MUST be private
3. Legal is currently recommending all repositories include the MIT License
4. Before a repository is move from a private to public repository legal MUST sign off

---

Coding Recommendations

1. Comment code assuming someone else will leverage the code

• Assume you will not remember how you did something a couple months later

2. Use what ever language you feel appropriate (But python over perl...)
3. Code should when possible be designed for usage by others at TGen

• Don't use binaries in you $PATH or in your local directory
  • When ever possible use module load package/version or module add package/version
• Attempt to make all code username independent
  • Use relative paths or dynamically determine username

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Using GITHUB with Different IDEs or Terminal Enviroments

1. R Studio

Recommend this book from Jenny Bryan - https://happygitwithr.com/

2. PyCharm

3. Terminal

Cloning the repository

git clone "repository"
# The "repository" can be copied from the repository website
# Copy the link under the "Clone or Download" button
# This version is the SSH version there is also an HTTPS version
git clone git@github.com:tgen/Institutional_Instructions.git

Now that is downloaded move into the local version of the repository

cd Institutional_Instructions/

Now pull down the most recent version

git pull
# Likely get the following message the first time, before modifying you should "pull" to get most recent code
Already up-to-date.

MODIFY THE FILES YOU NEED TO MODIFY

IF YOU CREATED NEW FILES YOU WILL NEED TO "ADD" THEM BEFORE COMMITTING AND PUSHING

git add Message.sh
    
git add file OR git add folder
#Add gender test folder
git add gender_test/
#Add all files in gender test folder
git add gender_test/*

Commit the changes AND add a comment

git commit -am "your comment about what you changed"
git commit -am "Added message file for example ADD, COMMIT, and PUSH"

Then to push the update to the github website

git push #this pushes your changes to github
git push

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Markdown Cheatsheet

Headers Code:

# Header 1
## Header 2
### Header 3
#### Header 4
##### Header 5
###### Header 6

Headers Code Example:

Header 1

Header 2

Header 3

Header 4

Header 5

Header 6

Separator Code:

Text Above
---
Three or more dashes/hyphens, creates thin line
****
Three or more astericks, creates thick line
_____
Three or more underscores, creates thicker line?

Separator Code Example:

Text Above

Three or more dashes/hyphens, creates thin line

---

Three or more astericks, creates thick line

---

Three or more underscores, creates thicker line?

Emphasis Code:

NOTE: Each line, except last, ends with two spaces "  " to prevent wrapping  
Bold - **Bold** or __Bold__ (double asterisks or underscores)  
Italics - *Italics* or _Italics_ (single asterisks or underscores)  
Strikethrough - ~~Strikethrough~~ (double tildes)

Emphasis Code Example:

NOTE: Each line, except last, ends with two spaces " " to prevent wrapping
Bold - Bold or Bold (double asterisks or underscores)
Italics - Italics or Italics (single asterisks or underscores)
Strikethrough - Strikethrough (double tildes)

List Code:

1. Keats Lab (Ordered Sub-list)
  1. Wet Lab (Two indent spaces)
    1. Martin (Four indent spaces)
    2. Brooks
  2. Informatics (Ordered sub-list with letters)
    1. Austin
    2. Christophe
    3. Megan
    4. Jessica
    5. Sara
2. Liang Lab (Unordered sub-list, can use "*", "-", or "+")
  * Winnie
  - Lori
  + Jonathan

List Code Example:

1. Keats Lab (Ordered Sub-list)
2. Wet Lab (Two indent spaces) 1. Martin (Four indent spaces) 2. Brooks
3. Informatics (Ordered sub-list with letters) 1. Austin 2. Christophe 3. Megan 4. Jessica 5. Sara
4. Liang Lab (Unordered sub-list, can use "*", "-", or "+")

• Winnie

• Lori

• Jonathan

Table Code:

Note: Tables columns are defined by pipes (|), the header row is defined by inserting at least 3 hyphens (---) on the line below. You can set the alignment of each column using colons (:) on the header defining row, left (:---), center (:---:), right (---:). You can align things with spaces but it will occur automatically in the simple version below

Gene | Chromosome | Cancer Gene | Note
:--- | :---: | ---: | ---
TRAF3 | 14 | Yes | col1 left aligned
WHSC1L1 | 8 | No | col2 centered
RB1 | 13 | Yes | col3 right aligned

Table Code Example:

Gene	Chromosome	Cancer Gene	Note
TRAF3	14	Yes	col1 left aligned
WHSC1L1	8	No	col2 centered
RB1	13	Yes	col3 right aligned

Code Block Code:

Note: Code blocks can be indicated by either 4 spaces (" ") or above and below wrapped with three back ticks (```). The advantage of back ticks is it allows the definition of the code type so language specific syntax coloring can occur. In the example below the set of code blocks are indented with four spaces and then the back ticks used in the example are shown.

```python
s = "Python syntax highlighting"
print(s)
```

```bash
i="Bash syntax highlighting"
echo ${i}
exit 1
```

```javascript
var s = "JavaScript syntax highlighting";
alert(s);
```

```
No language indicated, so no syntax highlighting. 
But let's throw in a <b>tag</b>.
```

Code Block Example:

s = "Python syntax highlighting"
print(s)

i="Bash syntax highlighting"
echo ${i}
exit 1

var s = "JavaScript syntax highlighting";
alert(s);

No language indicated, so no syntax highlighting. 
But let's throw in a <b>tag</b>.