From 723f018f89c97bc54661b8c20eef330947b66798 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 5 Aug 2024 11:20:37 +1000
Subject: [PATCH 01/39] Add .venv to .gitignore
---
.gitignore | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitignore b/.gitignore
index 1d411e88..b3bcca6c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ mkdocs/
.DS_Store
mkdocs_dev/
venv
+.venv
From 78890b77c8509ccb756c98f257d8b97467948a89 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 5 Aug 2024 11:31:35 +1000
Subject: [PATCH 02/39] Remove mdx_showable extension
- Also remove \showable tags
This extension is deprecated and is causing errors when building the page
---
.../rna_seq_dge_advanced/rna_seq_advanced_tutorial.md | 4 ----
docs/tutorials/rna_seq_dge_basic/rna_seq_basic_tuxedo.md | 8 --------
mkdocs.yml | 1 -
3 files changed, 13 deletions(-)
diff --git a/docs/tutorials/rna_seq_dge_advanced/rna_seq_advanced_tutorial.md b/docs/tutorials/rna_seq_dge_advanced/rna_seq_advanced_tutorial.md
index 6dd3cff3..cd183316 100644
--- a/docs/tutorials/rna_seq_dge_advanced/rna_seq_advanced_tutorial.md
+++ b/docs/tutorials/rna_seq_dge_advanced/rna_seq_advanced_tutorial.md
@@ -512,8 +512,6 @@ In the Galaxy tool panel, under NGS Analysis, select
2. Examine the Differential_Counts_DESeq2.html file. This file has some
output logs and plots from running DESeq2. Take a look at the PCA plot.
-\showable{More info on PCA plots}{hint}
-
PCA plots are useful for exploratory data analysis. Samples which are more
similar to each other are expected to cluster together. A count matrix often
has thousands of dimensions (one for each feature) and our PCA plot generated in
@@ -531,8 +529,6 @@ For both conditions, the 3 replicates tend to be closer to each other than they
Additionally, within conditions, the lower glucose (chem) condition shows more
variability between replicates than the higher glucose (batch) condition.
-\endshowable
-
#### 3. Filter out the significant differentially expressed genes.
Under Basic Tools, click on **Filter and Sort > Filter**:
diff --git a/docs/tutorials/rna_seq_dge_basic/rna_seq_basic_tuxedo.md b/docs/tutorials/rna_seq_dge_basic/rna_seq_basic_tuxedo.md
index bfe800be..30d0003d 100644
--- a/docs/tutorials/rna_seq_dge_basic/rna_seq_basic_tuxedo.md
+++ b/docs/tutorials/rna_seq_dge_basic/rna_seq_basic_tuxedo.md
@@ -253,12 +253,8 @@ In the left tool panel menu, under NGS Analysis, select
- Use defaults for the other fields
- Execute
-\showable{Show screenshot}{hint}
-
-\endshowable
-
Note: This may take a few minutes, depending on how busy the server is.
@@ -432,12 +428,8 @@ In the left tool panel menu, under NGS Analysis, select
- Use defaults for the other fields
- Execute
-\showable{Show screenshot}{hint}
-
-\endshowable
-
#### 3. Explore the Cuffdiff output files
diff --git a/mkdocs.yml b/mkdocs.yml
index 92ca267d..e85bda58 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -85,7 +85,6 @@ extra_templates: [
]
markdown_extensions:
- 'markdown_include.include'
- - 'mdx_showable'
- 'markdown.extensions.fenced_code'
- admonition
- smarty
From 9de05c6b468e48fc37c05f7cf59bab33634d34a2 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 6 Aug 2024 14:01:16 +1000
Subject: [PATCH 03/39] Drafting new tutorial
---
docs/tutorials/git_new/git.md | 69 +++++++++++++++++++++++++++++++++++
1 file changed, 69 insertions(+)
create mode 100644 docs/tutorials/git_new/git.md
diff --git a/docs/tutorials/git_new/git.md b/docs/tutorials/git_new/git.md
new file mode 100644
index 00000000..007ad793
--- /dev/null
+++ b/docs/tutorials/git_new/git.md
@@ -0,0 +1,69 @@
+# Version control with Git
+
+## Setup
+**Install Git**
+**Create a GitHub account**
+**Configuring Git**
+
+## Overview
+
+**Topic**
+
+* [ ] Genomics
+* [ ] Transcriptomics
+* [ ] Proteomics
+* [ ] Metabolomics
+* [ ] Statistics and visualisation
+* [ ] Structural Modelling
+* [x] Basic skills
+
+
+**Skill level**
+
+* [x] Beginner
+* [ ] Intermediate
+* [ ] Advanced
+
+**Data:** TBD
+
+**Tools:** TBD
+
+**Pipeline:** TBD
+
+**Learning objectives:** TBD
+
+## Introduction
+
+### 1. What is Git?
+- Distributed version control system created by Linus Torvalds.
+
+### 2. Why use version control?
+- Backing up your code
+- Sharing your code
+ - Packaging and distribution
+- Documenting your work
+- Collaborating
+ - The "Lingua Franca" of software engineering
+- Why Git will make you a better researcher
+ - You know you can always go back to a working version of your code
+ - You will have a digital lab notebook
+ - You will have a way of showcasing your projects
+ - You will be able to distribute your code to others
+ - You will be able to modify other peoples' code and make contributions to it
+
+### 3. Basic concepts
+- Repositories
+ - Remotes (basic-level only)
+- Commits
+ - Snapshots of a repository
+- The staging area
+
+## Your first Git repository
+
+### The Git directory
+
+### Tracking changes
+- The staging area
+ - `git add` and `git commit`
+- What makes a good commit?
+ - Writing good commit messages
\ No newline at end of file
From a06c1c288f83b13b0e6605f18bf7a77b4a280254 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Wed, 7 Aug 2024 11:36:04 +1000
Subject: [PATCH 04/39] Add overview and setup sections to GitHub workshop
---
docs/tutorials/git_new/git.md | 69 ++++++++++++++++++++++++++++++-----
1 file changed, 60 insertions(+), 9 deletions(-)
diff --git a/docs/tutorials/git_new/git.md b/docs/tutorials/git_new/git.md
index 007ad793..c8f052e5 100644
--- a/docs/tutorials/git_new/git.md
+++ b/docs/tutorials/git_new/git.md
@@ -1,10 +1,5 @@
# Version control with Git
-## Setup
-**Install Git**
-**Create a GitHub account**
-**Configuring Git**
-
## Overview
**Topic**
@@ -24,13 +19,68 @@
* [ ] Intermediate
* [ ] Advanced
-**Data:** TBD
+**Data:** None required, we will create our own code repository.
+
+**Tools:** Git `>=2.40`
+
+**Pipeline:**
+*Section 1:* What is Git? And why use it?
+*Section 2:* Creating your first Git repository
+*Section 3:* Incorporating Git into your day-to-day work
+
+**Learning objectives:** learn the basics of version control, how to track changes and how to collaborate.
+
+## Setup
+**Install Git**
+
+If you have Anaconda, changes are you already have Git installed. Open either a Terminal or an Anaconda
+Prompt, and type `git --version`. If you are already have Git installed, it will show the version number.
+Otherwise, you can install it with `conda install git -y`. If you don't have Anaconda or conda installed,
+you can follow the instructions for [your operating system here.](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
+
+**Create a GitHub account**
+
+The next step will be to create a GitHub account. If you already have one, skip this step. Otherwise, head
+over to [GitHub](https://github.com/) and click the "Sign Up" button at the top right. Make sure you [verify
+your email address.](https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-email-preferences/verifying-your-email-address#troubleshooting-email-verification)
+
+!!! success
+ The two steps above are all that are required before the workshop. You can complete the following steps during the workshop.
+
+**SSH access (optional)**
+
+We strongly recommend that *at some point* you [configure SSH access to your GitHub account.](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account).
+Otherwise, it will ask for your password every time you try to interact with GitHub. This is OK, but can
+be annoying after some time. See below on how to connect with SSH.
+
+??? note "Configuring SSH access for GitHub"
+ 1. Make sure you have `openssl` installed by typing `openssl --version` in the Terminal.
+ - You can install it with `conda install openssl` if not installed.
+ 2. Make sure your ssh-agent is running with ```eval `ssh-agent` ```.
+ 3. Create a new SSH key with `ssh-keygen`.
+ 4. Add the key to your SSH-agent with `ssh-add `, for example `ssh-add /home/username/.ssh/id_rsa`.
+ 5. Print your **public** key by typing `cat .pub`, for example `cat /home/username/.ssh/id_rsa.pub`.
+ 6. On GitHub, click your profile icon on the top right, then Settings > SSH and GPG keys > New SSH key > paste your **public** key and give it a meaningful name.
+ 7. Test SSH access with `ssh -T git@github.com`. It should print a message like this: `Hi ! You've successfully authenticated, but GitHub does not provide shell access.`
+
+**Configuring Git**
+
+The final step in setting up Git is adding your user name and email to the Git configuration. This is required
+because Git documents our work, that is, who did what. It is also a requirement for your GitHub authentication,
+especially if you haven't set up SSH access.
+
+!!! warning "Important"
+ Use the same email that you used to sign up to GitHub.
+
+ If you prefer to keep your email private, you can [set up a noreply address with GitHub](https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-email-preferences/setting-your-commit-email-address).
-**Tools:** TBD
+Go to your Terminal and type:
-**Pipeline:** TBD
+``` bash
+git config --global user.name "FirstName LastName"
+git config --global user.email "your@email.com"
+```
-**Learning objectives:** TBD
## Introduction
@@ -44,6 +94,7 @@
- Documenting your work
- Collaborating
- The "Lingua Franca" of software engineering
+ - Will be required if you want to work in coding projects with other people (including past and future you!)
- Why Git will make you a better researcher
- You know you can always go back to a working version of your code
- You will have a digital lab notebook
From ffc8c869591c048b899ea479e6e38793e96811d3 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Wed, 7 Aug 2024 13:11:47 +1000
Subject: [PATCH 05/39] Working on introduction
---
docs/tutorials/git_new/git.md | 21 ++++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
diff --git a/docs/tutorials/git_new/git.md b/docs/tutorials/git_new/git.md
index c8f052e5..926c6cf2 100644
--- a/docs/tutorials/git_new/git.md
+++ b/docs/tutorials/git_new/git.md
@@ -27,6 +27,7 @@
*Section 1:* What is Git? And why use it?
*Section 2:* Creating your first Git repository
*Section 3:* Incorporating Git into your day-to-day work
+*Section 4:* Leveraging the best out of GitHub
**Learning objectives:** learn the basics of version control, how to track changes and how to collaborate.
@@ -44,8 +45,8 @@ The next step will be to create a GitHub account. If you already have one, skip
over to [GitHub](https://github.com/) and click the "Sign Up" button at the top right. Make sure you [verify
your email address.](https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-email-preferences/verifying-your-email-address#troubleshooting-email-verification)
-!!! success
- The two steps above are all that are required before the workshop. You can complete the following steps during the workshop.
+!!! success "You are all set for now."
+ The two steps above are all that are required **before** the workshop. You can complete the following steps during the workshop.
**SSH access (optional)**
@@ -81,11 +82,25 @@ git config --global user.name "FirstName LastName"
git config --global user.email "your@email.com"
```
+!!! success "Well done!"
+ You are ready to start using Git.
## Introduction
### 1. What is Git?
-- Distributed version control system created by Linus Torvalds.
+A concise definition is that Git is a **version control system**. It was developed in the early 2000s by
+Linus Torvalds, the person behind the Linux kernel, and other members of the Linux community. In fact, the initial purpose of
+Git was to support the development and updates of the Linux kernel.
+
+Git is attractive because of several things:
+
+* It's **fully distributed**. What this means is that several (hundreds, thousands) of users can work on the same project in a streamlined way.
+* It's **blazing fast**. Because (nearly) every operation that Git performs is local, everything works almost instantaneously.
+* It has **integrity**. Git checksums data before storing it, so it's impossible to change the content of files without knowing about it.
+
+This is all well and good, but let's try to understand what version control means for us as researchers.
+
+
### 2. Why use version control?
- Backing up your code
From 2b1773166cd95a1cc070fc206d31363b0818091f Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Fri, 6 Sep 2024 10:27:05 +1000
Subject: [PATCH 06/39] Progressing on new Git workshop
---
docs/tutorials/git_new/git.md | 40 ++++++++++++++++++++++++++---------
1 file changed, 30 insertions(+), 10 deletions(-)
diff --git a/docs/tutorials/git_new/git.md b/docs/tutorials/git_new/git.md
index 926c6cf2..e531060c 100644
--- a/docs/tutorials/git_new/git.md
+++ b/docs/tutorials/git_new/git.md
@@ -24,10 +24,10 @@
**Tools:** Git `>=2.40`
**Pipeline:**
-*Section 1:* What is Git? And why use it?
-*Section 2:* Creating your first Git repository
-*Section 3:* Incorporating Git into your day-to-day work
-*Section 4:* Leveraging the best out of GitHub
+*Section 1:* Introduction
+*Section 2:* Your first Git repository
+*Section 3:* Collaborating with Git
+*Section 4:* Tips and best practices
**Learning objectives:** learn the basics of version control, how to track changes and how to collaborate.
@@ -87,22 +87,22 @@ git config --global user.email "your@email.com"
## Introduction
-### 1. What is Git?
+### What is Git?
A concise definition is that Git is a **version control system**. It was developed in the early 2000s by
Linus Torvalds, the person behind the Linux kernel, and other members of the Linux community. In fact, the initial purpose of
Git was to support the development and updates of the Linux kernel.
Git is attractive because of several things:
-* It's **fully distributed**. What this means is that several (hundreds, thousands) of users can work on the same project in a streamlined way.
-* It's **blazing fast**. Because (nearly) every operation that Git performs is local, everything works almost instantaneously.
+* It is **fully distributed**. What this means is that several (hundreds, thousands) of users can work on the same project in a streamlined way.
+* It is **blazing fast**. Because (nearly) every operation that Git performs is local, everything works almost instantaneously.
* It has **integrity**. Git checksums data before storing it, so it's impossible to change the content of files without knowing about it.
This is all well and good, but let's try to understand what version control means for us as researchers.
-### 2. Why use version control?
+### Why use version control?
- Backing up your code
- Sharing your code
- Packaging and distribution
@@ -117,7 +117,7 @@ This is all well and good, but let's try to understand what version control mean
- You will be able to distribute your code to others
- You will be able to modify other peoples' code and make contributions to it
-### 3. Basic concepts
+### Basic concepts
- Repositories
- Remotes (basic-level only)
- Commits
@@ -132,4 +132,24 @@ This is all well and good, but let's try to understand what version control mean
- The staging area
- `git add` and `git commit`
- What makes a good commit?
- - Writing good commit messages
\ No newline at end of file
+ - Writing good commit messages
+
+### Remotes: pushing and pulling
+
+## Collaborating with Git
+
+### Cloning a repository
+
+### Cloning versus forking
+
+### Submitting a pull request
+
+### Reviewing a pull request
+
+## Tips and best practices
+
+### How to incorporate Git in your day-to-day work
+
+### Leveraging the GitHub interface
+
+### Do's and Dont's
From f780e5fa97e64639914dd72238d98a428bece561 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Fri, 6 Sep 2024 11:53:19 +1000
Subject: [PATCH 07/39] Add VS Code code-workspace files to .gitignore
---
.gitignore | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitignore b/.gitignore
index b3bcca6c..f2a47ca1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ mkdocs/
mkdocs_dev/
venv
.venv
+*.code-workspace
From ea306984d92ff057b91dc43a0ffd9187ef40aea6 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Fri, 6 Sep 2024 13:21:20 +1000
Subject: [PATCH 08/39] Finish 'What is Git' section
- Add 'media/' directory
---
docs/tutorials/git_new/git.md | 116 ++++++++-
docs/tutorials/git_new/media/merge.svg | 122 ++++++++++
docs/tutorials/git_new/media/phd101212s.png | Bin 0 -> 83764 bytes
docs/tutorials/git_new/media/versions.svg | 247 ++++++++++++++++++++
4 files changed, 480 insertions(+), 5 deletions(-)
create mode 100644 docs/tutorials/git_new/media/merge.svg
create mode 100644 docs/tutorials/git_new/media/phd101212s.png
create mode 100644 docs/tutorials/git_new/media/versions.svg
diff --git a/docs/tutorials/git_new/git.md b/docs/tutorials/git_new/git.md
index e531060c..7b48c0cc 100644
--- a/docs/tutorials/git_new/git.md
+++ b/docs/tutorials/git_new/git.md
@@ -24,12 +24,16 @@
**Tools:** Git `>=2.40`
**Pipeline:**
-*Section 1:* Introduction
+*Section 1:* Introduction
*Section 2:* Your first Git repository
-*Section 3:* Collaborating with Git
-*Section 4:* Tips and best practices
+*Section 3:* Collaborating with Git
+*Section 4:* Tips and best practices
-**Learning objectives:** learn the basics of version control, how to track changes and how to collaborate.
+**Learning objectives:** learn the basics of version control, how to track changes in a repository and how to collaborate using Git.
+
+!!! warning "Disclaimer"
+ This tutorial is partially based on the [Software Carpentry's Git Novice lesson](https://swcarpentry.github.io/git-novice/). Some portions have been directly copied from that lesson, while others have been fully rewritten.
+ The lesson is under a [CC-BY 4.0 license](https://swcarpentry.github.io/git-novice/LICENSE.html).
## Setup
**Install Git**
@@ -100,7 +104,88 @@ Git is attractive because of several things:
This is all well and good, but let's try to understand what version control means for us as researchers.
-
+
+
+“notFinal.doc” by Jorge Cham, [https://www.phdcomics.com](http://www.phdcomics.com/comics/archive/phd101212s.gif)
+
+---
+
+We've all been in this situation before: it seems unnecessary to have
+multiple nearly-identical versions of the same document. Some word
+processors let us deal with this a little better, such as Microsoft
+Word's
+[Track Changes](https://support.office.com/en-us/article/Track-changes-in-Word-197ba630-0f5f-4a8e-9a77-3712475e806a),
+Google Docs' [version history](https://support.google.com/docs/answer/190843?hl=en), or
+LibreOffice's [Recording and Displaying Changes](https://help.libreoffice.org/Common/Recording_and_Displaying_Changes).
+
+Version control systems start with a base version of the document and
+then record changes you make each step of the way. You can
+think of it as a recording of your progress: you can rewind to start at the base
+document and play back each change you made, eventually arriving at your
+more recent version.
+
+{alt='A diagram demonstrating how a single document grows as the result of sequential changes'}
+
+Once you think of changes as separate from the document itself, you
+can then think about "playing back" different sets of changes on the base document, ultimately
+resulting in different versions of that document. For example, two users can make independent
+sets of changes on the same document.
+
+{alt='A diagram with one source document that has been modified in two different ways to produce two different versions of the document'}
+
+Unless multiple users make changes to the same section of the document - a
+[conflict](./git.md#glossary) - you can
+incorporate two sets of changes into the same base document.
+
+{alt='A diagram that shows the merging of two different document versions into one document that contains all of the changes from both versions'}
+
+A version control system is a tool that keeps track of these changes for us,
+effectively creating different versions of our files. It allows us to decide
+which changes will be made to the next version (each record of these changes is
+called a [commit](./git.md#glossary), and keeps useful metadata
+about them. The complete history of commits for a particular project and their
+metadata make up a [repository](./git.md#glossary).
+Repositories can be kept in sync across different computers, facilitating
+collaboration among different people.
+
+??? note "The Long History of Version Control Systems"
+
+ Automated version control systems are nothing new.
+ Tools like [RCS](https://en.wikipedia.org/wiki/Revision_Control_System), [CVS](https://en.wikipedia.org/wiki/Concurrent_Versions_System), or [Subversion](https://en.wikipedia.org/wiki/Apache_Subversion) have been around since the early 1980s and are used by
+ many large companies.
+ However, many of these are now considered legacy systems (i.e., outdated) due to various
+ limitations in their capabilities.
+ More modern systems, such as Git and [Mercurial](https://swcarpentry.github.io/hg-novice/),
+ are *distributed*, meaning that they do not need a centralized server to host the repository.
+ These modern systems also include powerful merging tools that make it possible for
+ multiple authors to work on
+ the same files concurrently.
+
+!!! attention "Paper Writing"
+
+ - Imagine you drafted an excellent paragraph for a paper you are writing, but later ruin it. How would you retrieve the *excellent* version of your conclusion? Is it even possible?
+
+ - Imagine you have 5 co-authors. How would you manage the changes and comments they make to your paper? If you use LibreOffice Writer or Microsoft Word, what happens if you accept changes made using the `Track Changes` option? Do you have a history of those changes?
+
+ ??? example "Solution"
+
+ - Recovering the excellent version is only possible if you created a copy
+ of the old version of the paper. The danger of losing good versions
+ often leads to the problematic workflow illustrated in the PhD Comics
+ cartoon at the top of this page.
+
+ - Collaborative writing with traditional word processors is cumbersome.
+ Either every collaborator has to work on a document sequentially
+ (slowing down the process of writing), or you have to send out a
+ version to all collaborators and manually merge their comments into
+ your document. The 'track changes' or 'record changes' option can
+ highlight changes for you and simplifies merging, but as soon as you
+ accept changes you will lose their history. You will then no longer
+ know who suggested that change, why it was suggested, or when it was
+ merged into the rest of the document. Even online word processors like
+ Google Docs or Microsoft Office Online do not fully resolve these
+ problems.
+
### Why use version control?
- Backing up your code
@@ -153,3 +238,24 @@ This is all well and good, but let's try to understand what version control mean
### Leveraging the GitHub interface
### Do's and Dont's
+
+#### Do
+- Write good commit messages
+ - Say **why**, not **what** you changed
+- Make small changes
+- Commit often
+- Think about the reviewer
+- Document as you code
+
+#### Don't
+- Make vague commit messages
+- Accumulate unrelated changes in a single commit
+- Let things go stale – delete or "stash" them
+
+## Glossary
+
+**Conflict:**
+
+**Commit:**
+
+**Repository:**
\ No newline at end of file
diff --git a/docs/tutorials/git_new/media/merge.svg b/docs/tutorials/git_new/media/merge.svg
new file mode 100644
index 00000000..bc1378cb
--- /dev/null
+++ b/docs/tutorials/git_new/media/merge.svg
@@ -0,0 +1,122 @@
+
+
+
\ No newline at end of file
diff --git a/docs/tutorials/git_new/media/phd101212s.png b/docs/tutorials/git_new/media/phd101212s.png
new file mode 100644
index 0000000000000000000000000000000000000000..c47c428bdea0921aa9ed078c4830fb73ba8bce38
GIT binary patch
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zszKPj7#_j1$U-=wc*5zQm%
-\endshowable
-
Note: This may take a few minutes, depending on how busy the server is.
@@ -432,12 +428,8 @@ In the left tool panel menu, under NGS Analysis, select
- Use defaults for the other fields
- Execute
-\showable{Show screenshot}{hint}
-
-\endshowable
-
#### 3. Explore the Cuffdiff output files
diff --git a/mkdocs.yml b/mkdocs.yml
index 92ca267d..e85bda58 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -85,7 +85,6 @@ extra_templates: [
]
markdown_extensions:
- 'markdown_include.include'
- - 'mdx_showable'
- 'markdown.extensions.fenced_code'
- admonition
- smarty
From 9de05c6b468e48fc37c05f7cf59bab33634d34a2 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 6 Aug 2024 14:01:16 +1000
Subject: [PATCH 03/39] Drafting new tutorial
---
docs/tutorials/git_new/git.md | 69 +++++++++++++++++++++++++++++++++++
1 file changed, 69 insertions(+)
create mode 100644 docs/tutorials/git_new/git.md
diff --git a/docs/tutorials/git_new/git.md b/docs/tutorials/git_new/git.md
new file mode 100644
index 00000000..007ad793
--- /dev/null
+++ b/docs/tutorials/git_new/git.md
@@ -0,0 +1,69 @@
+# Version control with Git
+
+## Setup
+**Install Git**
+**Create a GitHub account**
+**Configuring Git**
+
+## Overview
+
+**Topic**
+
+* [ ] Genomics
+* [ ] Transcriptomics
+* [ ] Proteomics
+* [ ] Metabolomics
+* [ ] Statistics and visualisation
+* [ ] Structural Modelling
+* [x] Basic skills
+
+
+**Skill level**
+
+* [x] Beginner
+* [ ] Intermediate
+* [ ] Advanced
+
+**Data:** TBD
+
+**Tools:** TBD
+
+**Pipeline:** TBD
+
+**Learning objectives:** TBD
+
+## Introduction
+
+### 1. What is Git?
+- Distributed version control system created by Linus Torvalds.
+
+### 2. Why use version control?
+- Backing up your code
+- Sharing your code
+ - Packaging and distribution
+- Documenting your work
+- Collaborating
+ - The "Lingua Franca" of software engineering
+- Why Git will make you a better researcher
+ - You know you can always go back to a working version of your code
+ - You will have a digital lab notebook
+ - You will have a way of showcasing your projects
+ - You will be able to distribute your code to others
+ - You will be able to modify other peoples' code and make contributions to it
+
+### 3. Basic concepts
+- Repositories
+ - Remotes (basic-level only)
+- Commits
+ - Snapshots of a repository
+- The staging area
+
+## Your first Git repository
+
+### The Git directory
+
+### Tracking changes
+- The staging area
+ - `git add` and `git commit`
+- What makes a good commit?
+ - Writing good commit messages
\ No newline at end of file
From a06c1c288f83b13b0e6605f18bf7a77b4a280254 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Wed, 7 Aug 2024 11:36:04 +1000
Subject: [PATCH 04/39] Add overview and setup sections to GitHub workshop
---
docs/tutorials/git_new/git.md | 69 ++++++++++++++++++++++++++++++-----
1 file changed, 60 insertions(+), 9 deletions(-)
diff --git a/docs/tutorials/git_new/git.md b/docs/tutorials/git_new/git.md
index 007ad793..c8f052e5 100644
--- a/docs/tutorials/git_new/git.md
+++ b/docs/tutorials/git_new/git.md
@@ -1,10 +1,5 @@
# Version control with Git
-## Setup
-**Install Git**
-**Create a GitHub account**
-**Configuring Git**
-
## Overview
**Topic**
@@ -24,13 +19,68 @@
* [ ] Intermediate
* [ ] Advanced
-**Data:** TBD
+**Data:** None required, we will create our own code repository.
+
+**Tools:** Git `>=2.40`
+
+**Pipeline:**
+*Section 1:* What is Git? And why use it?
+*Section 2:* Creating your first Git repository
+*Section 3:* Incorporating Git into your day-to-day work
+
+**Learning objectives:** learn the basics of version control, how to track changes and how to collaborate.
+
+## Setup
+**Install Git**
+
+If you have Anaconda, changes are you already have Git installed. Open either a Terminal or an Anaconda
+Prompt, and type `git --version`. If you are already have Git installed, it will show the version number.
+Otherwise, you can install it with `conda install git -y`. If you don't have Anaconda or conda installed,
+you can follow the instructions for [your operating system here.](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
+
+**Create a GitHub account**
+
+The next step will be to create a GitHub account. If you already have one, skip this step. Otherwise, head
+over to [GitHub](https://github.com/) and click the "Sign Up" button at the top right. Make sure you [verify
+your email address.](https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-email-preferences/verifying-your-email-address#troubleshooting-email-verification)
+
+!!! success
+ The two steps above are all that are required before the workshop. You can complete the following steps during the workshop.
+
+**SSH access (optional)**
+
+We strongly recommend that *at some point* you [configure SSH access to your GitHub account.](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account).
+Otherwise, it will ask for your password every time you try to interact with GitHub. This is OK, but can
+be annoying after some time. See below on how to connect with SSH.
+
+??? note "Configuring SSH access for GitHub"
+ 1. Make sure you have `openssl` installed by typing `openssl --version` in the Terminal.
+ - You can install it with `conda install openssl` if not installed.
+ 2. Make sure your ssh-agent is running with ```eval `ssh-agent` ```.
+ 3. Create a new SSH key with `ssh-keygen`.
+ 4. Add the key to your SSH-agent with `ssh-add