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Draft Guide to ARCfs
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--- | ||
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 | ||
--- | ||
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## About this guide | ||
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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. | ||
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<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> | ||
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<br> | ||
<br> | ||
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## Before we can start | ||
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: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 | ||
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## Create an access token in DataHUB | ||
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![image](./../img/ARCfs_KB_01_blurred_marked.png) | ||
![image](./../img/ARCfs_KB_02_blurred_marked.png) | ||
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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. | ||
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: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. | ||
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## Add the token to Galaxy | ||
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![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) | ||
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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. | ||
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: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. | ||
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## Data import | ||
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With the token available to Galaxy, you are now able to import data. You can do this as described below. | ||
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![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) | ||
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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. | ||
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## Data export | ||
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It is also possible to export datasets back to an ARC. You can do this as described below. | ||
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![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) | ||
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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. |
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Original file line number | Diff line number | Diff line change |
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--- | ||
layout: docs | ||
title: Work with your ARC | ||
date: 2024-01-23 | ||
add toc: true | ||
add support: false | ||
add sidebar: _sidebars/mainSidebar.md | ||
--- | ||
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In this section you can find guides on how to work with your ARC. |
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