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docs/02-bringing_own_data.md

@@ -7,8 +7,6 @@
 # Uploading from the Cloud {#uploading-cloud}
 
 Imagine your lab has some data stored in a Google bucket. Maybe you want to bring this data into AnVIL for analysis, and you want the data to be associated with a specific workspace. One option for doing this is to copy the data from the existing Google bucket to a bucket that is specifically associated with an AnVIL workspace.
-
-In this example, we'll upload some genomic data into AnVIL that is currently stored in the cloud (specifically, in a Google bucket).
 <br><br>
 
 ::: {.dictionary}
@@ -17,7 +15,11 @@ In this example, we'll upload some genomic data into AnVIL that is currently sto
 You can read more about how data is saved in the cloud [here](https://support.terra.bio/hc/en-us/articles/360034335332-Understanding-data-in-the-Cloud)!
 :::
 
-We're going to upload some fastq files for a SARS-CoV-2 sample. The bucket we're accessing contains 5 samples: 
+In this example, we'll upload some genomic data into AnVIL that is currently stored in the cloud (specifically, in a Google bucket).
+
+
+We're going to upload some fastq files for a SARS-CoV-2 sample. 
+The bucket we're accessing contains 5 samples: 
 
 * two compressed fastq files
 * a fasta file for a SARS-CoV-2 reference genome
@@ -27,7 +29,15 @@ The bucket ID (URI) is `fc-80d0e1cd-61e9-472f-b1bd-c6a8223bd1cd`.
 
 For this activity, you will retrieve the two uncompressed fastq files and upload them into your workspace.
 
-<img src="02-bringing_own_data_files/figure-html//1lSUfsg_oja-Iqq5pTFD1VOuR32GLUq2l-sCBYNO3OTg_g3afa908e330_0_178.png" alt="Image shows the contents of a Google bucket used in the SARS-CoV-2 on Galaxy activity." width="100%" />
+::: {.notice}
+_Genetics_
+
+**Novice**: no genetics skills needed
+
+_Programming skills_
+
+**Intermediate**: some command line programming skills needed
+:::
 
 ::: {.notice}
 **What will this cost?**
@@ -164,7 +174,7 @@ When you are done with your session, click on the Jupyter icon in the right-side
 - Delete the computing environment when you are finished with your session
 
 
-# Additional Resources
+## Additional Resources
 
 You can read documentation about bringing your own data to AnVIL on the [Portal](https://anvilproject.org/learn/find-data/bringing-your-own-data)
 

docs/404.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2026-01-13" />
+<meta name="date" content="2026-02-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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@@ -106,12 +106,12 @@
 <li class="chapter" data-level="2.4" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-four-verify-that-files-have-been-transferred"><i class="fa fa-check"></i><b>2.4</b> Step Four: Verify that files have been transferred</a></li>
 <li class="chapter" data-level="2.5" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-five-delete-your-environment-when-you-are-done-with-your-session"><i class="fa fa-check"></i><b>2.5</b> Step Five: Delete your environment when you are done with your session</a></li>
 <li class="chapter" data-level="2.6" data-path="uploading-cloud.html"><a href="uploading-cloud.html#summary"><i class="fa fa-check"></i><b>2.6</b> Summary</a></li>
+<li class="chapter" data-level="2.7" data-path="uploading-cloud.html"><a href="uploading-cloud.html#additional-resources"><i class="fa fa-check"></i><b>2.7</b> Additional Resources</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="additional-resources.html"><a href="additional-resources.html"><i class="fa fa-check"></i><b>3</b> Additional Resources</a></li>
 <li class="part"><span><b>Appendix</b></span></li>
 <li class="chapter" data-level="" data-path="give-us-feedback.html"><a href="give-us-feedback.html"><i class="fa fa-check"></i>Give us Feedback</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
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docs/About.md

@@ -53,7 +53,7 @@ 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     2026-01-13
+##  date     2026-02-06
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
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docs/about-the-authors.html

@@ -22,7 +22,7 @@
 
 
 
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@@ -106,12 +106,12 @@
 <li class="chapter" data-level="2.4" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-four-verify-that-files-have-been-transferred"><i class="fa fa-check"></i><b>2.4</b> Step Four: Verify that files have been transferred</a></li>
 <li class="chapter" data-level="2.5" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-five-delete-your-environment-when-you-are-done-with-your-session"><i class="fa fa-check"></i><b>2.5</b> Step Five: Delete your environment when you are done with your session</a></li>
 <li class="chapter" data-level="2.6" data-path="uploading-cloud.html"><a href="uploading-cloud.html#summary"><i class="fa fa-check"></i><b>2.6</b> Summary</a></li>
+<li class="chapter" data-level="2.7" data-path="uploading-cloud.html"><a href="uploading-cloud.html#additional-resources"><i class="fa fa-check"></i><b>2.7</b> Additional Resources</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="additional-resources.html"><a href="additional-resources.html"><i class="fa fa-check"></i><b>3</b> Additional Resources</a></li>
 <li class="part"><span><b>Appendix</b></span></li>
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 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
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 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
@@ -290,7 +290,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
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-##  date     2026-01-13
+##  date     2026-02-06
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
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docs/give-us-feedback.html

@@ -22,14 +22,14 @@
 
 
 
-<meta name="date" content="2026-01-13" />
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   <link rel="shortcut icon" href="assets/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
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@@ -106,12 +106,12 @@
 <li class="chapter" data-level="2.4" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-four-verify-that-files-have-been-transferred"><i class="fa fa-check"></i><b>2.4</b> Step Four: Verify that files have been transferred</a></li>
 <li class="chapter" data-level="2.5" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-five-delete-your-environment-when-you-are-done-with-your-session"><i class="fa fa-check"></i><b>2.5</b> Step Five: Delete your environment when you are done with your session</a></li>
 <li class="chapter" data-level="2.6" data-path="uploading-cloud.html"><a href="uploading-cloud.html#summary"><i class="fa fa-check"></i><b>2.6</b> Summary</a></li>
+<li class="chapter" data-level="2.7" data-path="uploading-cloud.html"><a href="uploading-cloud.html#additional-resources"><i class="fa fa-check"></i><b>2.7</b> Additional Resources</a></li>
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-<li class="chapter" data-level="3" data-path="additional-resources.html"><a href="additional-resources.html"><i class="fa fa-check"></i><b>3</b> Additional Resources</a></li>
 <li class="part"><span><b>Appendix</b></span></li>
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-<li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
@@ -172,7 +172,7 @@ <h1>Give us Feedback<a href="give-us-feedback.html#give-us-feedback" class="anch
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docs/index.html

@@ -22,7 +22,7 @@
 
 
 
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@@ -106,12 +106,12 @@
 <li class="chapter" data-level="2.4" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-four-verify-that-files-have-been-transferred"><i class="fa fa-check"></i><b>2.4</b> Step Four: Verify that files have been transferred</a></li>
 <li class="chapter" data-level="2.5" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-five-delete-your-environment-when-you-are-done-with-your-session"><i class="fa fa-check"></i><b>2.5</b> Step Five: Delete your environment when you are done with your session</a></li>
 <li class="chapter" data-level="2.6" data-path="uploading-cloud.html"><a href="uploading-cloud.html#summary"><i class="fa fa-check"></i><b>2.6</b> Summary</a></li>
+<li class="chapter" data-level="2.7" data-path="uploading-cloud.html"><a href="uploading-cloud.html#additional-resources"><i class="fa fa-check"></i><b>2.7</b> Additional Resources</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="additional-resources.html"><a href="additional-resources.html"><i class="fa fa-check"></i><b>3</b> Additional Resources</a></li>
 <li class="part"><span><b>Appendix</b></span></li>
 <li class="chapter" data-level="" data-path="give-us-feedback.html"><a href="give-us-feedback.html"><i class="fa fa-check"></i>Give us Feedback</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
@@ -149,7 +149,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Data on AnVIL</h1>
-<p class="date"><em>January 13, 2026</em></p>
+<p class="date"><em>February 06, 2026</em></p>
 </div>
 <div id="about-this-book" class="section level1 unnumbered hasAnchor">
 <h1>About this Book<a href="index.html#about-this-book" class="anchor-section" aria-label="Anchor link to header"></a></h1>

docs/index.md

@@ -1,6 +1,6 @@
 ---
 title: "Data on AnVIL"
-date: "January 13, 2026"
+date: "February 06, 2026"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: book.bib

docs/introduction.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2026-01-13" />
+<meta name="date" content="2026-02-06" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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@@ -106,12 +106,12 @@
 <li class="chapter" data-level="2.4" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-four-verify-that-files-have-been-transferred"><i class="fa fa-check"></i><b>2.4</b> Step Four: Verify that files have been transferred</a></li>
 <li class="chapter" data-level="2.5" data-path="uploading-cloud.html"><a href="uploading-cloud.html#step-five-delete-your-environment-when-you-are-done-with-your-session"><i class="fa fa-check"></i><b>2.5</b> Step Five: Delete your environment when you are done with your session</a></li>
 <li class="chapter" data-level="2.6" data-path="uploading-cloud.html"><a href="uploading-cloud.html#summary"><i class="fa fa-check"></i><b>2.6</b> Summary</a></li>
+<li class="chapter" data-level="2.7" data-path="uploading-cloud.html"><a href="uploading-cloud.html#additional-resources"><i class="fa fa-check"></i><b>2.7</b> Additional Resources</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="additional-resources.html"><a href="additional-resources.html"><i class="fa fa-check"></i><b>3</b> Additional Resources</a></li>
 <li class="part"><span><b>Appendix</b></span></li>
 <li class="chapter" data-level="" data-path="give-us-feedback.html"><a href="give-us-feedback.html"><i class="fa fa-check"></i>Give us Feedback</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
+<li class="chapter" data-level="3" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>3</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
 <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>