Merge branch 'main' of https://github.com/jhudsl/Adv_Reproducibility_…

…in_Cancer_Informatics into main

docs/03-version-control-with-github.md

@@ -27,7 +27,7 @@ GitKraken is nice because they have lots of nice tutorials, it works pretty well
 
 ### Install GitKraken
 
-[Go here to install GitKraken](https://support.gitkraken.com/how-to-install/).
+[Go here to install GitKraken](https://www.gitkraken.com/).
 
 Follow their instructions to sign in with your GitHub account. It will ask you to authorize your GitHub account to connect to GitKraken. Click `Authorize`.
 
@@ -67,7 +67,7 @@ Depending on whether you prefer to use R or Python, you can choose to follow thi
 
 
 
-Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc)).
+Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 
 </details>
@@ -77,7 +77,7 @@ Now double click your chapter zip file to unzip. For Windows you may have to [fo
 
 
 
-Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc)).
+Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 
 </details>
@@ -91,8 +91,6 @@ Now double click your chapter zip file to unzip. For Windows you may have to [fo
   - Choose `add a README`.
 - Follow [these instructions](https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github) to add all the files that are inside the `reproducible-R-example.zip` or `reproducible-python-example.zip` file you downloaded to this new repository.
 
-This new repository you created should look [something like this](https://github.com/cansavvy/repository-name).
-
 ### git clone
 
 Now you have a repository on GitHub online!
@@ -196,7 +194,7 @@ One more note: if you do want to use the command line or if you want to know mor
 
 ## More resources for learning GitHub
 
-- [Happy Git and GitHub for the useR](https://happygitwithr.com/) by @Bryan2021.
+- [Happy Git and GitHub for the useR](https://happygitwithr.com) by @Bryan2021.
 - [GitHub for data scientists](https://towardsdatascience.com/introduction-to-github-for-data-scientists-2cf8b9b25fba) by @Vickery2019.
 - [Intro to GitHub](https://github.com/skills/introduction-to-github) by @GitHub2022.
 - [First Day on GitHub](https://skills.github.com/#first-day-on-github) by @GitHub2022c.

docs/04-data-handling.md

@@ -34,12 +34,12 @@ wget -h
 wget -O <FOLDER/FILE_TO_SAVE_TO> <URL>
 ```
 
-You can download this [general template download file here](https://raw.githubusercontent.com/AlexsLemonade/training-specific-template/main/working-with-your-data/template-scripts/wget-TEMPLATE.sh) [@Shapiro2021].
+You can download this [general template download file here](https://raw.githubusercontent.com/AlexsLemonade/training-specific-template/main/additional-resources/template-scripts/wget-TEMPLATE.sh) [@Shapiro2021].
 
 ### Examples of data download scripts
 
 - [Downloading data from GEO with GEOquery](http://genomicsclass.github.io/book/pages/GEOquery.html)
 - [Data download script for multiple files of the same place](https://github.com/AlexsLemonade/training-modules/blob/master/machine-learning/setup/00-data-download.sh)
 - [Data download script - refine.bio example](https://github.com/jhudsl/reproducible-R-example/blob/main/00-download-data.py)
 
-For more about data sharing techniques, see the [Ethical Data Handling for Cancer Research](https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/) course</a>.
+For more about data sharing techniques, see the [Ethical Data Handling for Cancer Research](https://github.com/fhdsl/Ethical_Data_Handling_for_Cancer_Research) course</a>.

docs/08-modifying-docker-image.md

@@ -23,7 +23,7 @@ To see what images you have on your internet repository, you can log on to docke
 
 ![](resources/images/08-modifying-docker-image_files/figure-docx//1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I_gfc8849fa4d_0_38.png){width=100%}
 
-After you sign into dockerhub, you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button.
+After you sign into dockerhub, click on the `Repositories` tab, so you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button.
 
 ![](resources/images/08-modifying-docker-image_files/figure-docx//1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I_gfc8849fa4d_0_10.png){width=100%}
 
@@ -38,7 +38,7 @@ It will tell you `Last pushed: never`. On the right it will tell you the command
 
 Go to your [local command line](https://towardsdatascience.com/a-quick-guide-to-using-command-line-terminal-96815b97b955) and use the command specified on the right side of your repository page. You don't have to specify a tagname if you don't want to.  If you don't want to specify a tagname, leave off the `:tagname` if you like.
 
-Now you will be able to test pulling your image using `docker pull <image name>` like we did in the previous chapter.
+Now you will be able to test pulling your image using `docker pull <image name>` like we did in the previous chapter. You can also click on the `Public View` button to copy the pull command for your Docker image.
 
 Docker images can be pulled from being stored online but these images are built originally from a `Dockerfile`.
 
@@ -129,7 +129,7 @@ If all built successfully, you should see a message like:
 => => naming to docker.io/library/image_name
 ```
 
-Now to run the image we can use the docker run command we used in the previous chapter and we should have a message: `Yay! I added to this Docker image` pop up upon building.
+Now to run the image we can use the docker run command we used in the previous chapter (see below) and we should have a message: `Yay! I added to this Docker image` pop up upon building.
 
 <details> <summary> To run your new **Python docker image** </summary>
 But replace `image_name` with whatever you have called your image.

docs/About.md

@@ -46,7 +46,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2022-12-21                  
+##  date     2024-03-12                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version    date       lib source                            

docs/about-the-authors.html

@@ -388,7 +388,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2022-12-21                  
+##  date     2024-03-12                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version    date       lib source                            

docs/index.html

@@ -264,7 +264,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Advanced Reproducibility in Cancer Informatics</h1>
-<p class="date"><em>December, 2022</em></p>
+<p class="date"><em>March, 2024</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>

docs/index.md

@@ -1,6 +1,6 @@
 ---
 title: "Advanced Reproducibility in Cancer Informatics"
-date: "December, 2022"
+date: "March, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib, packages.bib]

docs/modifying-a-docker-image.html

@@ -278,15 +278,15 @@ <h2><span class="header-section-number">8.2</span> Managing images</h2>
 <p>To see what images you have on your internet repository, you can log on to dockerhub.
 <a href="https://hub.docker.com/">Go here to login (or create a username if you have not yet)</a>.</p>
 <p><img src="resources/images/08-modifying-docker-image_files/figure-html/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I_gfc8849fa4d_0_38.png" title="The dockerhub login page." alt="The dockerhub login page." width="100%" /></p>
-<p>After you sign into dockerhub, you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button.</p>
+<p>After you sign into dockerhub, click on the <code>Repositories</code> tab, so you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button.</p>
 <p><img src="resources/images/08-modifying-docker-image_files/figure-html/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I_gfc8849fa4d_0_10.png" title="In your dockerhub main page, you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button." alt="In your dockerhub main page, you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button." width="100%" /></p>
 <p>Upon adding the new repository to dockerhub, you will need name it the same as whatever you are calling it locally. You can put a description and name and click create. On the right it shows how you can interact with this from your local command line.</p>
 <p><img src="resources/images/08-modifying-docker-image_files/figure-html/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I_gfc8849fa4d_0_48.png" title="Upon adding the new repository to dockerhub, you will need name it the same as whatever you are calling it locally. You can put a description and name and click create. On the right it shows how you can interact with this from your local command line." alt="Upon adding the new repository to dockerhub, you will need name it the same as whatever you are calling it locally. You can put a description and name and click create. On the right it shows how you can interact with this from your local command line." width="100%" /></p>
 <p>After you’ve created the image repository, you will be brought to the image repository page.
 It will tell you <code>Last pushed: never</code>. On the right it will tell you the command you will need in order to push the image to dockerhub.</p>
 <p><img src="resources/images/08-modifying-docker-image_files/figure-html/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I_gfc8849fa4d_0_56.png" title="After you've created the image repository, you will be brought to the image repository page. It will tell you Last pushed: never. On the right it will tell you the command you will need in order to push the image to dockerhub." alt="After you've created the image repository, you will be brought to the image repository page. It will tell you Last pushed: never. On the right it will tell you the command you will need in order to push the image to dockerhub." width="100%" /></p>
 <p>Go to your <a href="https://towardsdatascience.com/a-quick-guide-to-using-command-line-terminal-96815b97b955">local command line</a> and use the command specified on the right side of your repository page. You don’t have to specify a tagname if you don’t want to. If you don’t want to specify a tagname, leave off the <code>:tagname</code> if you like.</p>
-<p>Now you will be able to test pulling your image using <code>docker pull &lt;image name&gt;</code> like we did in the previous chapter.</p>
+<p>Now you will be able to test pulling your image using <code>docker pull &lt;image name&gt;</code> like we did in the previous chapter. You can also click on the <code>Public View</code> button to copy the pull command for your Docker image.</p>
 <p>Docker images can be pulled from being stored online but these images are built originally from a <code>Dockerfile</code>.</p>
 </div>
 <div id="exercise-build-a-docker-image" class="section level2" number="8.3">
@@ -348,7 +348,7 @@ <h3><span class="header-section-number">8.3.4</span> Add to the Dockerfile</h3>
 =&gt; =&gt; exporting layers                                                    0.0s
 =&gt; =&gt; writing image sha256:ayuahgfuiseohfauwheufhauwihefuahweufhawfbuibe  0.0s
 =&gt; =&gt; naming to docker.io/library/image_name</code></pre>
-<p>Now to run the image we can use the docker run command we used in the previous chapter and we should have a message: <code>Yay! I added to this Docker image</code> pop up upon building.</p>
+<p>Now to run the image we can use the docker run command we used in the previous chapter (see below) and we should have a message: <code>Yay! I added to this Docker image</code> pop up upon building.</p>
 <details>
 <summary>
 To run your new <strong>Python docker image</strong>

docs/no_toc/03-version-control-with-github.md

@@ -27,7 +27,7 @@ GitKraken is nice because they have lots of nice tutorials, it works pretty well
 
 ### Install GitKraken
 
-[Go here to install GitKraken](https://support.gitkraken.com/how-to-install/).
+[Go here to install GitKraken](https://www.gitkraken.com/).
 
 Follow their instructions to sign in with your GitHub account. It will ask you to authorize your GitHub account to connect to GitKraken. Click `Authorize`.
 
@@ -62,7 +62,7 @@ Depending on whether you prefer to use R or Python, you can choose to follow thi
 
 
 
-Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc)).
+Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 
 </details>
@@ -72,7 +72,7 @@ Now double click your chapter zip file to unzip. For Windows you may have to [fo
 
 
 
-Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc)).
+Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 
 </details>
@@ -86,8 +86,6 @@ Now double click your chapter zip file to unzip. For Windows you may have to [fo
   - Choose `add a README`.
 - Follow [these instructions](https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github) to add all the files that are inside the `reproducible-R-example.zip` or `reproducible-python-example.zip` file you downloaded to this new repository.
 
-This new repository you created should look [something like this](https://github.com/cansavvy/repository-name).
-
 ### git clone
 
 Now you have a repository on GitHub online!
@@ -191,7 +189,7 @@ One more note: if you do want to use the command line or if you want to know mor
 
 ## More resources for learning GitHub
 
-- [Happy Git and GitHub for the useR](https://happygitwithr.com/) by @Bryan2021.
+- [Happy Git and GitHub for the useR](https://happygitwithr.com) by @Bryan2021.
 - [GitHub for data scientists](https://towardsdatascience.com/introduction-to-github-for-data-scientists-2cf8b9b25fba) by @Vickery2019.
 - [Intro to GitHub](https://github.com/skills/introduction-to-github) by @GitHub2022.
 - [First Day on GitHub](https://skills.github.com/#first-day-on-github) by @GitHub2022c.

docs/no_toc/04-data-handling.md

@@ -34,12 +34,12 @@ wget -h
 wget -O <FOLDER/FILE_TO_SAVE_TO> <URL>
 ```
 
-You can download this [general template download file here](https://raw.githubusercontent.com/AlexsLemonade/training-specific-template/main/working-with-your-data/template-scripts/wget-TEMPLATE.sh) [@Shapiro2021].
+You can download this [general template download file here](https://raw.githubusercontent.com/AlexsLemonade/training-specific-template/main/additional-resources/template-scripts/wget-TEMPLATE.sh) [@Shapiro2021].
 
 ### Examples of data download scripts
 
 - [Downloading data from GEO with GEOquery](http://genomicsclass.github.io/book/pages/GEOquery.html)
 - [Data download script for multiple files of the same place](https://github.com/AlexsLemonade/training-modules/blob/master/machine-learning/setup/00-data-download.sh)
 - [Data download script - refine.bio example](https://github.com/jhudsl/reproducible-R-example/blob/main/00-download-data.py)
 
-For more about data sharing techniques, see the [Ethical Data Handling for Cancer Research](https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/) course</a>.
+For more about data sharing techniques, see the [Ethical Data Handling for Cancer Research](https://github.com/fhdsl/Ethical_Data_Handling_for_Cancer_Research) course</a>.