Merge pull request #51 from jhudsl/small_edits

adding some edits that might help learners

03-version-control-with-github.Rmd

@@ -33,7 +33,7 @@ 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`.
 
@@ -77,7 +77,7 @@ mkdir -p chapter-zips
 wget -O chapter-zips/reproducible-python-example.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/reproducible-python-example.zip
 ```
 
-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).
 
 ```{bash, include = FALSE}
 unzip -o chapter-zips/reproducible-python-example.zip -d chapter-zips/
@@ -92,7 +92,7 @@ mkdir -p chapter-zips
 wget -O chapter-zips/reproducible-R-example.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/reproducible-R-example.zip
 ```
 
-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).
 
 ```{bash, include = FALSE}
 unzip -o chapter-zips/reproducible-R-example.zip -d chapter-zips/
@@ -108,8 +108,6 @@ unzip -o chapter-zips/reproducible-R-example.zip -d chapter-zips/
   - 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!
@@ -241,7 +239,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6
 
 ## 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.

04-data-handling.Rmd

@@ -38,12 +38,12 @@ 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>.

08-modifying-docker-image.Rmd

@@ -31,7 +31,7 @@ To see what images you have on your internet repository, you can log on to docke
 ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I/edit#slide=id.gfc8849fa4d_0_38")
 ```
 
-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.
 
 ```{r, fig.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.", out.width = "100%", echo = FALSE}
 ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I/edit#slide=id.gfc8849fa4d_0_10")
@@ -52,7 +52,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6
 
 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`.
 
@@ -143,7 +143,7 @@ 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.

resources/exclude_files.txt

@@ -0,0 +1,7 @@
+About.Rmd
+docs/*
+style-sets/*
+manuscript/*
+LICENSE.md
+README.md
+code_of_conduct.md