Update external links. Resolves #709.

content/about/platform/hca.md

@@ -8,7 +8,7 @@ The Human Cell Atlas (HCA) is a collaborative community of international scienti
 
 The HCA registry has more than one thousand member scientists from hundreds of institutions around the world. The project is steered and governed by an Organizing Committee, co-chaired by Aviv Regev and Sarah Teichmann.
 
-To learn more about the HCA, visit https://www.humancellatlas.org/.
+To learn more about the HCA, visit <https://www.humancellatlas.org>.
 
-To join the HCA community, you can register on this page: https://www.humancellatlas.org/joinHCA
+To join the HCA community, you can register on this page: <https://www.humancellatlas.org/join-hca>
 

content/contact/contact/contact-us.md

@@ -14,7 +14,7 @@ Find something that’s not working right?  Have questions about the Data Portal
 
 ## Register with the HCA
 
-Register with the Human Cell Atlas to find collaborators and stay up-to-date about news and events.  [Register with the HCA](https://www.humancellatlas.org/joinHCA).
+Register with the Human Cell Atlas to find collaborators and stay up-to-date about news and events.  [Register with the HCA](https://www.humancellatlas.org/join-hca).
 
 ## Contribute to the HCA
 

content/document/creating-content/content-style-guide.md

@@ -93,7 +93,7 @@ Commonly used contractions like “don’t”, “it’s”, “isn’t”, “d
 
 * Each sentence, even a sentence fragment, should start with a capital letter and end with a period.
 
-* Keep paragraph size to 3-4 sentences OR LESS. Add subheadings to break up longer paragraphs, for ease of reading on the web. This page is a great example of using subheadings: https://dev.data.humancellatlas.org/about/platform/dcp/ingest-service
+* Keep paragraph size to 3-4 sentences OR LESS. Add subheadings to break up longer paragraphs, for ease of reading on the web.
 
 ### Graphics and Color
 * Make sure that the colors in your graphics are color-blind friendly.  There are many helpful articles online about choosing the best colors; for example, [How to Optimize Charts For Color Blind Readers Using Color Blind Friendly Palettes](https://venngage.com/blog/color-blind-friendly-palette/)

content/document/creating-content/using-images.md

@@ -22,7 +22,7 @@ To reference the image we use markdown like:
 ![Cell Image](../_images/jumbotron-cell-mobile.png "That Cell!")
 ```
 
-Note the `../images/` preceding the image name. This is required to tell the CMS where the image is.
+Note the `../_images/` preceding the image name. This is required to tell the CMS where the image is.
 
 This renders like:
 

content/guides/userguides/consumer-vignettes/export-to-terra.md

@@ -45,7 +45,7 @@ For more information about how to use the Dockstore, see the [Dockstore document
 Step one: finding BAM files with the HCA Data Explorer
 ------------------------------------------------------
 
-You can use the [HCA Data Explorer][explorer] to find data to export to Terra.
+You can use the <link-to-browser relativelink="/projects">HCA Data Explorer</link-to-browser> to find data to export to Terra.
 The Data Explorer lists projects with data available for download from the Data
 Store and lets you filter the data for a number of attributes.
 
@@ -147,8 +147,7 @@ run the Jupyter notebooks in that repository, including:
 
   [dcv]: <https://github.com/HumanCellAtlas/data-consumer-vignettes>
   [jupyterlab]: <https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906>
-  [quick-start-guide]: <https://data.humancellatlas.org/guides/quick-start-guide>
-  [explorer]: <https://data.humancellatlas.org/explore/projects>
+  [quick-start-guide]: </guides/quick-start-guide>
   [terra]: <https://terra.bio>
   [terra-support]: <https://support.terra.bio/hc/en-us>
   [terra-register]: <https://support.terra.bio/hc/en-us/articles/360028235911-How-to-register-for-a-Terra-account>

content/guides/userguides/consumer-vignettes/intro-to-downloading-and-analyzing.md

@@ -21,7 +21,7 @@ tutorials:
 
 ## Step one: finding BAM files with the HCA Data Explorer
 
-You can use the [HCA Data Explorer][explorer] to find data to download using
+You can use the <link-to-browser relativelink="/projects">HCA Data Explorer</link-to-browser> to find data to download using
 the HCA CLI tools. The Data Explorer lists projects with data available
 for download from the Data Store and lets you filter the data for a number of
 attributes.
@@ -112,7 +112,6 @@ There are many different ways to launch Jupyter Notebooks including:
 
 
   [login]: https://github.com/HumanCellAtlas/data-consumer-vignettes/blob/master/Login%20to%20the%20DSS/Log%20In.ipynb
-  [explorer]: https://data.humancellatlas.org/explore/projects
   [dcv]: https://github.com/HumanCellAtlas/data-consumer-vignettes
   [download-bam]: https://github.com/HumanCellAtlas/data-consumer-vignettes/tree/master/Download%20Any%20BAM%20File
   [pysam]: https://pysam.readthedocs.io/en/latest/api.html

content/pipelines/pipeline-development/processing-pipelines/building-pipelines.md

@@ -56,5 +56,5 @@ We welcome your feedback about our current pipelines and your ideas for developm
 You are also welcome to attend meetings and participate in Slack discussions about data processing pipelines. Here are some details:
 
 1. Analysis Community Biweekly meetings are held every other Tuesday at 11AM, Eastern Time; view the [Agenda](https://docs.google.com/document/d/1860cE2zk2baXYefu5-WzQM_p_uTGjph6dWnehiRaFDw/edit#heading=h.rt36ocexz2z5)
-2. Join the HCA Slack channels: go to [Join Slack](https://join-hca-slack.data.humancellatlas.org/) to obtain an invitation, and join the #secondary analysis channel.
+2. Join the HCA Slack channels: go to [Join Slack](https://humancellatlas.slack.com/join/shared_invite/zt-8xpzlu3k-P9M6bKwAJNx~YI_ACLdrFg#/) to obtain an invitation, and join the #secondary analysis channel.
 3. Attend DCP demos; contact us for the dates and times, and use [this link](https://meet.google.com/eoo-rdxp-kim) to join each meeting

content/releases/documentation/2020-mar/replicating-the-release-analysis.md

@@ -8,7 +8,7 @@ draft: true
 #  Replicating the March 2020 Release Analyses
 This tutorial covers how to process a gene matrix (in loom format) for clustering, differential expression, and visualization using the Cumulus workflow in a Terra workspace. It uses the same [methods](methods.md) outlined for the DCP March 2020 Release. 
 
-All projects for the release were divided into individual datasets which are listed on the DCP <link-to-browser relativelink="/releases/2020-mar">March 2020 Release</link-to-browser> page. For this tutorial, we use the sample dataset 2020-Mar-Landscape-Adult-Liver-10x derived from the project [“Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations”](https://data.humancellatlas.org/explore/projects/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674). You can explore other datasets and repeat these analyses on additional matrix files.
+All projects for the release were divided into individual datasets which are listed on the DCP <link-to-browser relativelink="/releases/2020-mar">March 2020 Release</link-to-browser> page. For this tutorial, we use the sample dataset 2020-Mar-Landscape-Adult-Liver-10x derived from the project <link-to-browser relativelink="/projects/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674">"Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations"</link-to-browser>. You can explore other datasets and repeat these analyses on additional matrix files.
 
 ## Downloading the gene matrix (loom format) for the example dataset
 To start your analyses, you will need to download the gene matrix from the DCP. For each dataset, this matrix was generated using a standardized DCP pipeline (Optimus or Smart-seq2). The matrix contains either gene counts (10x samples) or RSEM TPMS (Smart-seq2 datasets), in addition to important metadata, such as specimen and sample processing information. This file will be used as input for the Cumulus workflow.

content/releases/documentation/2020-mar/working-with-release-files.md

@@ -17,7 +17,7 @@ If you would like to know more about how these release files were generated, ple
 ## What are the release files?
 Descriptions of all the March 2020 Release files can be found in the table below. Each Release dataset has a unique Dataset ID which is listed on the March 2020 Release page in the “Dataset” column. This ID is used as a prefix for all Release dataset files. 
 
-Some March 2020 Release files are used for interactive visualization in Single Cell Portal (any file with a .scp demarcation). These files are only available in [Single Cell Portal](https://singlecell.broadinstitute.org/single_cell?scpbr=human-cell-atlas-march-2020-release) (SCP) and not on the HCA [Data Coordination Platform](https://data.humancellatlas.org/) (DCP). 
+Some March 2020 Release files are used for interactive visualization in Single Cell Portal (any file with a .scp demarcation). These files are only available in [Single Cell Portal](https://singlecell.broadinstitute.org/single_cell?scpbr=human-cell-atlas-march-2020-release) (SCP) and not on the HCA [Data Coordination Platform](/) (DCP).
 
 | File name | File location: DCP and/or SCP | Description | Format | 
 | --- | --- | --- | --- |
@@ -143,20 +143,20 @@ You can visualize or annotate DCP Release files by either using the existing Mar
 #### 1. Navigate to [Single Cell Portal](https://singlecell.broadinstitute.org/single_cell) and login.
 
 #### 2. Go to the profile drop-down menu and select Add Study.
-![image](_images/13_SCP_add_study.png)
+![image](../../_images/13_SCP_add_study.png)
 
 #### 3. Select a unique name for the study page and billing information. 
 If you want to import files from an existing Terra workspace, the billing information must match the billing information used on Terra. 
 
-![image](_images/14_SCP_new_study.png)
+![image](../../_images/14_SCP_new_study.png)
 
 #### 4. If you wish to import Terra workspace files, Select Yes for using an existing Terra workspace.
 
 #### 5. Enter the Terra workspace name in the “Existing Terra Workspace” field. 
 For the 2020-Mar-Landscape-Adult-Liver-10x example dataset used in the [analysis tutorial](replicating-the-release-analysis.md), you would type the name “2020-Mar-Landscape-Adult-Liver-10x”.
 
 #### 6. Scroll to the bottom of the page and select Create Study.
-![image](_images/15_Create_study.png)
+![image](../../_images/15_Create_study.png)
 
 #### 7. If using an existing Terra workspace, you will be prompted to select the files you would like to import. 
 
@@ -189,13 +189,13 @@ Each March 2020 Release dataset has a Single Cell Portal study page where you ca
 To visualize the annotated cells for a Release dataset, go to the Explore tab of the Single Cell Portal study and follow the instructions below:
 
 #### 1. Select the View Options gear icon in the upper right corner.
-![image](_images/17_SCP_explore_view_options.png)
+![image](../../_images/17_SCP_explore_view_options.png)
 
 #### 2. Open the Select Annotations drop-down menu.
-![image](_images/18_SCP_Select_annotation_v2.png)
+![image](../../_images/18_SCP_Select_annotation_v2.png)
 
 #### 3. Choose either `annotated_cell_identity.text` or `annotated_cell_identity.ontology_label`. 
-![image](_images/19_cell_type_annotations.png).
+![image](../../_images/19_cell_type_annotations.png).
 
 The `annotated_cell_identity.text` option will list the cell types defined by the project contributors. The `annotated_cell_identity.ontology_label` will list cell types that have been harmonized using ontology services.
 
@@ -204,9 +204,9 @@ The March 2020 Release offers a Global Gene Search option using Single Cell Port
 #### 1. Go to the [Single Cell Portal HCA Release](https://singlecell.broadinstitute.org/single_cell?scpbr=human-cell-atlas-march-2020-release) page.
 When you enter the page, you will be defaulted to the Search Studies tab of the landing page. 
 #### 2. Select the Search Genes tab.
-![image](_images/20_SCP_Release_page.png)
+![image](../../_images/20_SCP_Release_page.png)
 #### 3. Type in the gene of interest. 
-![image](_images/21_tmem119_search.png)
+![image](../../_images/21_tmem119_search.png)
 At the top of the search, the number of datasets that have a positive match for the gene will appear. Below the search, a graphical display of cell clusters containing the gene of interest will display for all datasets containing the gene. 
 
 ## Next steps