diff --git a/src/docs/_sidebars/mainSidebar.md b/src/docs/_sidebars/mainSidebar.md index 4ed3eee6c..3c3af67e5 100644 --- 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) + + # [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 new file mode 100644 index 000000000..9a707b0e7 --- /dev/null +++ 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. + + + UserAdvanced + ModeTutorial + + +
+
+ +## 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 index cbff65748..4eee5a5fd 100644 --- 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. \ No newline at end of file +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 new file mode 100644 index 000000000..924f8f229 --- /dev/null +++ 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. diff --git a/src/docs/img/ARCfs_KB_01_blurred_marked.png b/src/docs/img/ARCfs_KB_01_blurred_marked.png new file mode 100644 index 000000000..203fb212f Binary files /dev/null and b/src/docs/img/ARCfs_KB_01_blurred_marked.png differ diff --git a/src/docs/img/ARCfs_KB_02_blurred_marked.png b/src/docs/img/ARCfs_KB_02_blurred_marked.png new file mode 100644 index 000000000..68f597b48 Binary files /dev/null and b/src/docs/img/ARCfs_KB_02_blurred_marked.png differ diff --git a/src/docs/img/ARCfs_KB_03_blurred_marked.png b/src/docs/img/ARCfs_KB_03_blurred_marked.png new file mode 100644 index 000000000..22eb354d2 Binary files /dev/null and b/src/docs/img/ARCfs_KB_03_blurred_marked.png differ diff --git a/src/docs/img/ARCfs_KB_06_blurred_marked.png b/src/docs/img/ARCfs_KB_06_blurred_marked.png new file mode 100644 index 000000000..40ca49a84 Binary files /dev/null and b/src/docs/img/ARCfs_KB_06_blurred_marked.png differ diff --git a/src/docs/img/ARCfs_KB_07_blurred_marked_cut.png b/src/docs/img/ARCfs_KB_07_blurred_marked_cut.png new file mode 100644 index 000000000..8744f453b Binary files /dev/null and b/src/docs/img/ARCfs_KB_07_blurred_marked_cut.png differ diff --git a/src/docs/img/ARCfs_KB_08_cut_marked.png b/src/docs/img/ARCfs_KB_08_cut_marked.png new file mode 100644 index 000000000..f078d775d Binary files /dev/null and b/src/docs/img/ARCfs_KB_08_cut_marked.png differ diff --git a/src/docs/img/ARCfs_KB_09_marked.png b/src/docs/img/ARCfs_KB_09_marked.png new file mode 100644 index 000000000..30af91643 Binary files /dev/null and b/src/docs/img/ARCfs_KB_09_marked.png differ diff --git a/src/docs/img/ARCfs_KB_10_11_marked.png b/src/docs/img/ARCfs_KB_10_11_marked.png new file mode 100644 index 000000000..af06cba38 Binary files /dev/null and b/src/docs/img/ARCfs_KB_10_11_marked.png differ diff --git a/src/docs/img/ARCfs_KB_12_13_marked.png b/src/docs/img/ARCfs_KB_12_13_marked.png new file mode 100644 index 000000000..c8f8bcd34 Binary files /dev/null and b/src/docs/img/ARCfs_KB_12_13_marked.png differ diff --git a/src/docs/img/ARCfs_KB_14_15_marked.png b/src/docs/img/ARCfs_KB_14_15_marked.png new file mode 100644 index 000000000..1b0e1da5e Binary files /dev/null and b/src/docs/img/ARCfs_KB_14_15_marked.png differ diff --git a/src/docs/img/ARCfs_KB_16_17_marked.png b/src/docs/img/ARCfs_KB_16_17_marked.png new file mode 100644 index 000000000..141f05cb1 Binary files /dev/null and b/src/docs/img/ARCfs_KB_16_17_marked.png differ diff --git a/src/docs/img/ARCfs_KB_18_19_marked.png b/src/docs/img/ARCfs_KB_18_19_marked.png new file mode 100644 index 000000000..692c8e9b0 Binary files /dev/null and b/src/docs/img/ARCfs_KB_18_19_marked.png differ diff --git a/src/docs/img/ARCfs_KB_20_21_marked_1.png b/src/docs/img/ARCfs_KB_20_21_marked_1.png new file mode 100644 index 000000000..4dbd790bb Binary files /dev/null and b/src/docs/img/ARCfs_KB_20_21_marked_1.png differ