add documentation for Cyberduck iRODS client

docs_manual/source/_static/ext_tool_cyberduck/iRODS (CUBI SODAR).cyberduckprofile

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+    <dict>
+        <key>Protocol</key>
+        <string>irods</string>
+        <key>Vendor</key>
+        <string>BIH CUBI</string>
+        <key>Description</key>
+        <string>SODAR Data Store</string>
+        <key>Hostname Configurable</key>
+        <false/>
+        <key>Port Configurable</key>
+        <false/>
+        <key>Default Hostname</key>
+        <string>sodar.bihealth.org</string>
+        <key>Region</key>
+        <string>sodarZone</string>
+        <key>Default Port</key>
+        <string>1247</string>
+        <key>Username Placeholder</key>
+        <string>SODAR username</string>
+        <key>Password Placeholder</key>
+        <string>SODAR password</string>
+        <key>Authorization</key>
+        <string>PAM</string>
+        <key>Default Path</key>
+        <string>/sodarZone/home</string>
+    </dict>
+</plist>

docs_manual/source/ext_tool_cyberduck.rst

@@ -0,0 +1,56 @@
+.. _ext_tool_cyberduck:
+
+Cyberduck
+^^^^^^^^^
+
+Cyberduck is a libre network storage browser for Mac and Windows.
+It can be used to access the iRODS filesystem on SODAR directly.
+
+Installation & Setup
+====================
+
+1. Download the Cyberduck installer from this website:
+https://cyberduck.io/download/
+
+.. note::
+    While Cyberduck is generally free to use, it will ask you to
+    donate to the project by making a one-time license key purchase.
+
+2. Download the SODAR iRODS connection profile:
+   :download:`iRODS (CUBI SODAR).cyberduckprofile <_static/ext_tool_cyberduck/iRODS (CUBI SODAR).cyberduckprofile>`
+
+3. Install and start Cyberduck. Your screen should look like this:
+
+   .. image:: _static/ext_tool_cyberduck/Cyberduck_home_empty.png
+
+4. Import the downloaded Cyberduck profile by double-clicking or dragging it
+   onto the Cyberduck window. A new dialog should appear. Fill in your
+   SODAR username and password in the respective fields.
+
+   .. image:: _static/ext_tool_cyberduck/Cyberduck_new_profile.png
+
+
+Using Cyberduck
+====================
+
+1. Connect to SODAR iRODS by double-clicking on the newly saved bookmark.
+
+   .. image:: _static/ext_tool_cyberduck/Cyberduck_home_profile.png
+
+2. The file browser should list collections for all projects you have access too.
+   Navigate the directory tree like in any other file browser. The directory you're
+   currently in is shown in the top bar.
+
+   .. image:: _static/ext_tool_cyberduck/Cyberduck_irods_home.png
+
+3. You can also jump to a specific folder (i. e. iRODS path copied from SODAR) via
+   the “Go” > “Go to folder” menu.
+
+   .. image:: _static/ext_tool_cyberduck/Cyberduck_goto_folder.png
+
+4. Files and collections can be downloaded via the right-click menu. Uploads to the
+   current directory can be started via the action button on top or via the right-click menu.
+
+   .. image:: _static/ext_tool_cyberduck/Cyberduck_irods_download.png
+
+5. Click “Disconnect” in the top right corner once you are done.

docs_manual/source/index.rst

@@ -99,6 +99,7 @@ Table of Contents
 
     ext_tool_igv_setup
     ext_tool_igv_opening
+    ext_tool_cyberduck
     ext_tool_winscp
 
 .. toctree::