Merge pull request #344 from TetraW/main

Draft Guide to ARCfs
nfdi4plants · Jan 23, 2024 · bbc4fa1 · bbc4fa1
2 parents ce50c2f + b0b6722
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diff --git a/src/docs/_sidebars/mainSidebar.md b/src/docs/_sidebars/mainSidebar.md
@@ -105,6 +105,8 @@
 ### [Track publication status](/docs/DataHUB-Manual/datahub-data-publications-status.html)
 ### [Use your DOIs](/docs/DataHUB-Manual/datahub-data-publications-dois.html)
 
+<!-- ## [ARCfs Usage](/docs/ARCfs/ARCfs.html) -->
+
 # [Guides](/docs/guides/index.html)
 ## [ARC User Journey](/docs/guides/ARCUserJourney.html)
 ## [Create your ARC](/docs/guides/index-CreateYourARC.html)
@@ -123,6 +125,9 @@
 ### [DataPLANT account](/docs/guides/datahub_account.html)
 ### [Invite collaborators to your ARC](/docs/guides/datahub_InviteCollaborators.html)
 
+## [Work with your ARC](/docs/guides/index-WorkWithYourARC.html)
+### [Using ARCs with Galaxy](/docs/guides/ARCs-galaxy.html)
+
 ## [Recommended ARC practices](/docs/guides/index-RecommendedARCPractices.html)
 ### [Syncing recommendation](/docs/guides/arc_SyncingRecommendation.html)
 ### [Keep files from syncing to the DataHUB](/docs/guides/arc_gitignore.html)

diff --git a/src/docs/guides/ARCs-galaxy.md b/src/docs/guides/ARCs-galaxy.md
@@ -0,0 +1,98 @@
+---
+layout: docs
+title: Using ARCs with Galaxy
+date: 2024-01-23
+author:
+- name: Julian Weidhase
+  github: https://github.com/TetraW
+  orcid: https://orcid.org/0009-0005-7138-4763
+add toc: true
+add support: true
+add sidebar: _sidebars/mainSidebar.md
+---
+
+## About this guide
+
+In this guide we introduce how to access ARCs from Galaxy. To access the data of an ARC, you must first provide a DataHUB access token in Galaxy, which is used to authenticate Galaxy to DataHUB. To create a new token and add it to [Galaxy](https://usegalaxy.eu/), you can proceed as described below.
+
+<a href="./index.html">
+    <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
+    <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>
+</a>
+
+<br>
+<br>
+
+## Before we can start
+
+:ballot_box_with_check: You have created an ARC before using the [ARC Commander](./../implementation/ArcCommander.html) or [ARCitect](./../ARCitect-Manual/index.html)  
+:ballot_box_with_check: You have a [DataPLANT](https://register.nfdi4plants.org) account  
+
+## Create an access token in DataHUB
+
+![image](./../img/ARCfs_KB_01_blurred_marked.png)
+![image](./../img/ARCfs_KB_02_blurred_marked.png)
+
+1. Open the dropdown menu for your personal settings.
+2. Open the "Preferences" menu.
+3. Change to tab "Access Tokens".
+4. Choose a name for the new token.
+5. Set a expiration date.
+6. Select the authorization scope. 
+
+:bulb: Only the scopes "api" (for write access) and "read_api" (for read access) are relevant for ARCfs.  
+**Important:** After you crated the token, you can copy and view it. After you leave the
+site, you will **not** be able to do so again.
+
+## Add the token to Galaxy
+
+
+![image](./../img/ARCfs_KB_03_blurred_marked.png)
+![image](./../img/ARCfs_KB_06_blurred_marked.png)
+![image](./../img/ARCfs_KB_07_blurred_marked_cut.png)
+![image](./../img/ARCfs_KB_08_cut_marked.png)
+
+1. Visit [usegalaxy.eu](https://usegalaxy.eu/) and log in or create an account. It is possible to log in using your DataPlant account.
+2. Open the "User" drop down menu and
+3. select "Preferences".
+4. In the user preference settings, select "Manage Information".
+5. Copy your token into the "API read access token" field. This filed is located at the bottom of the "User preferences" menu. Click "Save" to adopt your changes.
+
+:bulb: Despite the name "API **read** access token", tokens with write access rights (like those with the scope "api") will also work or, respectively, are required.
+
+## Data import
+
+With the token available to Galaxy, you are now able to import data. You can do this as described below.
+
+![image](./../img/ARCfs_KB_09_marked.png)
+![image](./../img/ARCfs_KB_10_11_marked.png)
+![image](./../img/ARCfs_KB_12_13_marked.png)
+![image](./../img/ARCfs_KB_14_15_marked.png)
+
+1. Click on the "Upload Data".
+2. Pick "Choose remote files".
+3. Scroll down and select "DataPLANT DataHub ARRCs".
+4. Explore ARCs or
+5. search for a specific one.
+6. Inside an ARC, choose the file you want to import to Galaxy. Confirm with "Ok".
+7. Click start to begin the import process to Galaxy. This may take some time, depending
+   on the workload on the Galaxy server and the size of your file.
+
+## Data export
+
+It is also possible to export datasets back to an ARC. You can do this as described below.
+
+![image](./../img/ARCfs_KB_16_17_marked.png)
+![image](./../img/ARCfs_KB_18_19_marked.png)
+![image](./../img/ARCfs_KB_20_21_marked_1.png)
+
+
+1. On the left sidebar, open the menu "Send Data".
+2. Select "Export datasets" to remote files source.
+3. In the opening menu, select "DataPLANT DataHUB ARCs".
+4. Select or
+5. search for an ARC.
+6. Chose a directory inside an ARC where your dataset should be stored.
+7. Choose the dataset you want to export,
+8. Clock on "Run Tool" to start the export process. This may take some time, depending
+   on the workload on the Galaxy server and the size of your file.
diff --git a/src/docs/guides/index-Contribute.md b/src/docs/guides/index-Contribute.md
@@ -7,4 +7,4 @@ add support: false
 add sidebar: _sidebars/mainSidebar.md
 ---
 
-In this section you can find guides on how to contribute to the ARC endeavour.
+In this section you can find guides on how to contribute to the ARC endeavour.
diff --git a/src/docs/guides/index-WorkWithYourARC.md b/src/docs/guides/index-WorkWithYourARC.md
@@ -0,0 +1,10 @@
+---
+layout: docs
+title: Work with your ARC
+date: 2024-01-23
+add toc: true
+add support: false
+add sidebar: _sidebars/mainSidebar.md
+---
+
+In this section you can find guides on how to work with your ARC.
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