Separated quickstart guides into connecting and transferring docs

content/connecting/for_windows_users.md → content/connecting/putty.md

 +++
-title = "For Windows Users"
-description = "Quickstart for Windows Users"
+title = "Using PuTTY"
+description = "How to connect to HCC clusters using the PuTTY SSH client"
 weight = "20"
 +++
 
 ##### Use of Duo two-factor authentication is **required** to access HCC resources. 
 ##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}).
----
 
-
-- [Access to HCC Supercomputers] (#access-to-hcc-supercomputers)
+- [Connecting to HCC Clusters](#connecting-to-hcc-clusters)
  - [For Windows 10 Users](#windows-10)
  - [For Windows 7 and 8.1 Users](#windows-7-and-8-1)
-- [File Transferring with HCC Supercomputers] (#file-transferring)
- - [SCP - Command Line] (#scp)
- - [WinSCP - GUI] (#winscp)
-- [Tutorial Video](#tutorial-video)
- 
-Access to HCC Supercomputers
--------------------------------
+
+## Connecting to HCC Clusters
 
 {{% notice info %}}
-If you are on a Mac, please use the quickstart for [For Mac/Linux
-Users]({{< relref "/connecting/for_maclinux_users" >}}).
+If you have a MacOS or Linux system, please see [Connecting with Terminal]
+({{< relref "/connecting/terminal.md" >}}).
 {{% /notice %}}
 
 
 ### Windows 10
 --------------
-For Windows 10 users, use the Command Prompt, accessed by entering `cmd` in the start menu, to access to the
-HCC supercomputers. In the Command Prompt,
-type `ssh <username>@tusker.unl.edu` and the corresponding password
-to get access to the HCC cluster **Tusker**. Note that &lt;username&gt;
-should be replaced by your HCC account username. If you do not have a
-HCC account, please contact a HCC specialist
-({{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu))
-or go to http://hcc.unl.edu/newusers.
-To use the **Crane** cluster, replace tusker.unl.edu with crane.unl.edu.
-
-{{< highlight bash >}}
-C:\> ssh <username>@tusker.unl.edu
-C:\> <password>
-{{< /highlight >}}
-
 
+Newer Windows users (Windows 10 build version 1803 and later), can connect using the
+Command Prompt. Please see [Connecting with the Terminal]({{< relref "/connecting/terminal" >}})
+for more details.
 
 ### Windows 7 and 8.1
 --------------
-This quick start will help you configure your personal computer to work
-with the HCC supercomputers. Here we use the two third party application
-**PuTTY** and **WinSCP** for demonstration.
 
-PuTTY: https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
-or [Direct Link](https://the.earth.li/~sgtatham/putty/latest/w32/putty.exe)
+For users with older Windows versions, you will need to install an SSH client to connect.
+We will cover the use of PuTTY here, but you are free to use any compatable client, such as 
+[MobaXterm]({{< relref "/connecting/mobaxterm" >}}) as well.
 
+To download and install PuTTY, visit the [PuTTY website]
+(https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html).
 
-Here we use the HCC cluster **Tusker** for demonstration. To use the
-**Crane** or cluster, replace `tusker.unl.edu` with `crane.unl.edu`.
+Once you have PuTTY installed, run the application and follow these steps:
+
+{{% notice info %}}
+**Note that the example below uses the `Tusker` cluster, which is no longer active.
+Replace all instances of `tusker` with either `crane` or `rhino` depending on which cluster
+you want to connect to.
+{{% /notice %}}
 
 1.  On the first screen, type `tusker.unl.edu` for Host Name, then click
     **Open**. 
     {{< figure src="/images/3178523.png" height="450" >}}
+
 2.  On the second screen, click on **Yes**.  
     {{< figure src="/images/3178524.png" height="300" >}}
+
 3.  On the third screen, enter your HCC account **username**. If you do
     not have a HCC account, please contact an HCC specialist
     ({{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu))
@@ -106,90 +94,13 @@ Here we use the HCC cluster **Tusker** for demonstration. To use the
 
     {{< figure src="/images/8127264.png" height="450" >}}
  
+### Next Steps:
 
-File Transferring with HCC Supercomputers
------------------------------------------
-
-{{% notice info%}}
-For best results when transfering data to and from the clusters, refer to [Handling Data]({{< ref "/handling_data" >}})
-{{%/notice%}}
-
-### SCP
-
-For Windows users, file transferring between your personal computer
-and the HCC supercomputers can be achieved through the command `scp`.
-Here we use **Tusker** for example. **The following commands should be
-executed from your computer. **
-
-**Uploading from local to remote**
-
-{{< highlight bash >}}
-C:\> scp -r .\<folder name> <username>@tusker.unl.edu:/work/<group name>/<username>
-{{< /highlight >}}
-
-The above command line transfers a folder from the current directory
-(`.\`) of the your computer to the `$WORK` directory of the HCC
-supercomputer, Tusker. Note that you need to replace `<group name>`
-and `<username>` with your HCC group name and username. 
-
-**Downloading from remote to local**
-
-{{< highlight bash >}}
-C:\> scp -r <username>@tusker.unl.edu:/work/<group name>/<username>/<folder name> .\
-{{< /highlight >}}
-
-The above command line transfers a folder from the `$WORK` directory of
-the HCC supercomputer, Tusker, to the current directory (`.\`) of the
-your computer.
-
-
-### WinSCP
-
-WinSCP: http://winscp.net/eng/download.php
-
-Usually it is convenient to upload and download files between your personal computer 
-and the HCC supercomputers through a Graphic User Interface (GUI).
-Download and install the third party application **WinSCP**
-to connect the file systems between your personal computer and the HCC supercomputers. 
-Below is a step-by-step installation guide. Here we use the HCC cluster **Tusker**
-for demonstration. To use the **Crane** cluster, replace `tusker.unl.edu`
-with `crane.unl.edu`.
-
-1.  On the first screen, type `tusker.unl.edu` for Host name, enter your
-    HCC account username and password for User name and Password. Then
-    click on **Login**.
-
-    {{< figure src="/images/3178530.png" height="450" >}}
-
-2.  On the second screen, click on **Yes**.  
-
-    {{< figure src="/images/3178531.png" >}}
-
-3.  Choose option "1" and press "Enter". Or simply press your Yubikey if
-    you have one.
-
-    {{< figure src="/images/8127268.png" >}}      
-
-4.  On the third screen, click on **Remote**. Under Remote, choose Go To
-    and Open Directory/Bookmark. Alternatively, you can use the keyboard
-    shortcut "Ctrl + O".
-
-    {{< figure src="/images/3178532.png" height="450" >}}
-
-5.  On the final screen, type `/work/<group name>/<username>` for Open
-    directory. Use your HCC group name and username to replace
-    `<group name>` and `<username>`. Then click on **OK**.  
-
-    {{< figure src="/images/3178533.png" height="450" >}}
-
-6.  Now you can drop and drag the files between your personal computer
-    and the HCC supercomputers.   
-    {{< figure src="/images/3178539.png" height="450" >}}
-
-Tutorial Video
---------------
-
-{{< youtube -Vh7SyC-3mA >}}
-
-
+Now that you are connected, check out these resources to learn more:
+ - [Handling Data]({{< relref "../handling_data/">}})
+ - [Running Applications]({{< relref "../applications/">}})
+ - [Submitting Jobs]({{< relref "../submitting_jobs/">}})
 
+If you are not familiar with using command line Linux, check out these resources:
+ - [Basic Linux Commands]({{< relref "basic_linux_commands">}})
+ - [Software Carpentry Introduction to the Unix Shell Lesson](http://swcarpentry.github.io/shell-novice/)

content/connecting/terminal.md

++++
+title = "Connecting with Terminal"
+description = "How to connect to HCC clusters using Terminal (Mac/Linux) or Command Prompt (Windows)"
+weight = "22"
++++
+
+##### Use of Duo two-factor authentication is **required** to access HCC resources.
+##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}).
+---
+- [Starting Terminal] (#starting-terminal)
+  - [MacOS](#macos)
+  - [Linux](#linux)
+  - [Windows](#windows)
+- [Connecting to HCC Clusters](#connecting-to-hcc-clusters)
+
+# Starting Terminal:
+
+## MacOS
+
+To start a terminal on MacOS, launch Spotlight by pressing `Command - spacebar`. 
+Type "Terminal" and press `enter` to launch the application. You should see a prompt, 
+which is a string of text, followed by a `$` or `>` character and a blinking cursor.
+Continue to connect by following the [connection directions below]
+(#connecting-to-hcc-clusters).
+
+## Linux
+
+Terminal can be opened on most Linux systems by pressing the `Ctrl + Alt + T` keys simultaneously.
+You should see a prompt - a string of text, followed by a `$` or `>` character and a blinking cursor.
+Continue to connect by following the [connection directions below](#connecting-to-hcc-clusters).
+
+
+## Windows
+
+Computers with newer versions of windows (Windows 10 build version 1803 and later), 
+can connect using the Command Prompt. To start the command prompt, open the start menu 
+and type `cmd`. Press `enter` to run. 
+You should see a prompt - a string of text, followed by a `$` or `>` character and a blinking cursor.
+Continue to connect by following the [connection directions below]
+(#connecting-to-hcc-clusters).
+
+If you are using an older versions of Windows, you will need to [download an SSH client]({{< relref "putty">}})
+
+### Connecting To HCC Clusters
+
+Once you have opened your terminal and you have a prompt, you can connect using the `ssh` command.
+For example, to connect to the Crane cluster type the following in your terminal or Command Prompt window:
+
+{{< highlight bash >}}
+$ ssh <username>@crane.unl.edu
+{{< /highlight >}}
+
+where `<username>` is replaced with your HCC account name. To use the **Rhino** cluster, 
+replace crane.unl.edu with rhino.unl.edu.
+
+The first time you connect to one of our clusters from a computer, you will be prompted to verify the connection:
+
+{{< highlight bash >}}
+The authenticity of host 'crane.unl.edu (129.93.227.113)' can't be established.
+RSA key fingerprint is SHA256:GDH3+iqSp3WJxtUE6tXNQcWRwpf0xjYgkQrYBDX3Ir0.
+RSA key fingerprint is MD5:e5:c5:ac:07:ff:47:53:18:5e:8b:44:16:51:78:4a:c7.
+Are you sure you want to continue connecting (yes/no)? 
+{{< /highlight >}}
+
+Type `yes` to indicate that you do intend to connect to Crane.
+
+You will then be prompted for your password. 
+
+{{% notice info %}}**Note that when entering your password, the characters you type will 
+not be displayed on screen for security reasons.**{{% /notice %}} 
+
+Once the account password is entered successfully, two-factor authentication prompt will appear. 
+
+{{< highlight bash >}}
+Duo two-factor login for demo01
+
+Enter a passcode or select one of the following options:
+
+ 1. Duo Push to XXX-XXX-4247
+ 2. Phone call to XXX-XXX-4247
+ 3. SMS passcodes to XXX-XXX-4247
+
+Passcode or option (1-3):
+{{< /highlight >}}
+
+Enter the number which corresponds to your preferred option. You will know you have connected 
+if your prompt changes to the following:
+
+{{< highlight bash >}}
+[<username>@login.crane ~]$ 
+{{< /highlight >}}
+
+### Next Steps:
+
+Now that you are connected, check out these resources to learn more:
+ - [Handling Data]({{< relref "../handling_data/">}})
+ - [Running Applications]({{< relref "../applications/">}})
+ - [Submitting Jobs]({{< relref "../submitting_jobs/">}})
+
+If you are not familiar with using command line Linux, check out these resources:
+ - [Basic Linux Commands]({{< relref "basic_linux_commands">}})
+ - [Software Carpentry Introduction to the Unix Shell Lesson](http://swcarpentry.github.io/shell-novice/)

content/connecting/for_maclinux_users.md → content/handling_data/data_transfer/cyberduck.md

 +++
-title = "For Mac/Linux Users"
-description = "Quickstart Guide for Mac/Linux Users"
+title = "File Transfer with CyberDuck (MacOS/Windows)"
+description = "Transfering data to and from HCC clusters with the Cyberduck SCP Client"
 weight = "22"
 +++
 
-##### Use of Duo two-factor authentication is **required** to access HCC resources.
-##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}).
 ---
-- [Access to HCC Supercomputers] (#access-to-hcc-supercomputers)
-- [File Transferring with HCC Supercomputers] (#file-transfering)
- - [SCP] (#using-the-scp-command)
- - [CyberDuck] (#using-cyberduck)
-- [Mac Tutorial Video](#mac-tutorial-video)
-- [Linux Tutorial Video](#linux-tutorial-video)
-
-This quick start will help you configure your personal computer to work
-with the HCC supercomputers.
-
-If you are running Windows, please use the quickstart [For Windows
-Users]({{< relref "/connecting/for_windows_users" >}}).
-
-Access to HCC Supercomputers
--------------------------------
-
-For Mac/Linux users, use the system program Terminal to access to the
-HCC supercomputers. In the Terminal prompt,
-type `ssh <username>@crane.unl.edu` and the corresponding password
-to get access to the HCC cluster **Crane**. Note that &lt;username&gt;
-should be replaced by your HCC account username. If you do not have a
-HCC account, please contact a HCC specialist
-({{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu))
-or go to https://hcc.unl.edu/newusers.
-To use the **Rhino** cluster, replace crane.unl.edu with with rhino.unl.edu.
 
-{{< highlight bash >}}
-$ ssh <username>@crane.unl.edu
-$ <password>
-{{< /highlight >}}
-
-File Transferring with HCC Supercomputers
------------------------------------------
-
-### Using the SCP command
-
-For Mac/Linux users, file transferring between your personal computer
-and the HCC supercomputers can be achieved through the command `scp`.
-Here we use **Crane** for example. **The following commands should be
-executed from your computer. **
-
-**Uploading from local to remote**
-
-{{< highlight bash >}}
-$ scp -r ./<folder name> <username>@crane.unl.edu:/work/<group name>/<username>
-{{< /highlight >}}
-
-The above command line transfers a folder from the current directory
-(`./`) of the your computer to the `$WORK` directory of the HCC
-supercomputer, Crane. Note that you need to replace `<group name>`
-and `<username>` with your HCC group name and username. 
-
-**Downloading from remote to local**
-
-{{< highlight bash >}}
-$ scp -r <username>@crane.unl.edu:/work/<group name>/<username>/<folder name> ./
-{{< /highlight >}}
-
-The above command line transfers a folder from the `$WORK` directory of
-the HCC supercomputer, Crane, to the current directory (`./`) of the
-your computer.
-
-### Using Cyberduck
+## Using Cyberduck
 ---------------
 
-If you wish to use a GUI, be aware that not all programs will function
+If you wish to use a GUI for data transfer, be aware that not all programs will function
 correctly with Duo two-factor authentication.  Mac users are recommended
 to use [Cyberduck](https://cyberduck.io). It is compatible with Duo, but a
 few settings need to be changed.
@@ -134,12 +71,3 @@ If you run into issues with two-factor authentication, try the command below for
 $ rm -rf ~/Library/ApplicationSupport/Cyberduck
 {{< /highlight >}}
 
-Mac Tutorial Video
-------------------
-
-{{< youtube ulfcmRGfqxU >}}
-
-Linux Tutorial Video
---------------------
-
-{{< youtube K0i3swpwtdc >}}

content/handling_data/data_transfer/scp.md

++++
+title = "File Transfer with scp"
+description = "Transfering data to and from HCC clusters with the scp command"
+weight = "22"
++++
+
+## Using the SCP command
+
+For MacOS, Linux, and later Windows users, file transferring between your personal computer
+and the HCC supercomputers can be achieved through the command `scp` which stands for secure copy.
+This method is ideal for quick transfer of smaller files. For large volume transfers,
+we recommend the using [Globus] or an SCP client such as [WinSCP for Windows]({{< relref "winscp">}}) or 
+[CyberDuck for Mac/Linux]({{< relref "cyberduck">}}).
+
+Just like the `cp` copy command, the `scp` command requires two arguments, 
+the path to source file(s) and the path to the target location.
+Since one or more of these locations are remote, you will need to specify the username and host for those.
+
+{{< highlight bash >}}
+$ scp <username>@<host>:<path_to_files> <username>@<host>:<path_to_files>
+{{< /highlight >}}
+
+For the local location, you do not need to specify the username or host. **When transferring to and from
+your local computer, the `scp` command should be ran on your computer, NOT from HCC clusters.**
+
+### Uploading a file to Crane
+
+Here is an example of file transfer to and from the Crane cluster.
+
+To upload the file `data.csv` in your current directory to your `$WORK` directory 
+on the Crane cluster, you would use the command:
+
+{{< highlight bash >}}
+$ scp ./data.csv <user_name>@crane.unl.edu:/work/<group_name>/<user_name>
+{{< /highlight >}}
+
+where `<user_name>` and `<group_name>` are replaced with your user name and your group name.
+
+### Downloading a file from Crane
+
+To download the file `data.csv` from your `$WORK` directory 
+on the Crane cluster to your current directory, you would use the command:
+
+{{< highlight bash >}}
+$ scp <user_name>@crane.unl.edu:/work/<group_name>/<user_name>/data.csv ./
+{{< /highlight >}}

content/handling_data/data_transfer/winscp.md

++++
+title = "For Windows Users"
+description = "Quickstart for Windows Users"
+weight = "20"
++++
+
+### WinSCP
+
+WinSCP: http://winscp.net/eng/download.php
+
+Usually it is convenient to upload and download files between your personal computer 
+and the HCC supercomputers through a Graphic User Interface (GUI).
+Download and install the third party application **WinSCP**
+to connect the file systems between your personal computer and the HCC supercomputers. 
+Below is a step-by-step installation guide. Here we use the HCC cluster **Tusker**
+for demonstration. To use the **Crane** cluster, replace `tusker.unl.edu`
+with `crane.unl.edu`.
+
+1.  On the first screen, type `tusker.unl.edu` for Host name, enter your
+    HCC account username and password for User name and Password. Then
+    click on **Login**.
+
+    {{< figure src="/images/3178530.png" height="450" >}}
+
+2.  On the second screen, click on **Yes**.  
+
+    {{< figure src="/images/3178531.png" >}}
+
+3.  Choose option "1" and press "Enter". Or simply press your Yubikey if
+    you have one.
+
+    {{< figure src="/images/8127268.png" >}}      
+
+4.  On the third screen, click on **Remote**. Under Remote, choose Go To
+    and Open Directory/Bookmark. Alternatively, you can use the keyboard
+    shortcut "Ctrl + O".
+
+    {{< figure src="/images/3178532.png" height="450" >}}
+
+5.  On the final screen, type `/work/<group name>/<username>` for Open
+    directory. Use your HCC group name and username to replace
+    `<group name>` and `<username>`. Then click on **OK**.  
+
+    {{< figure src="/images/3178533.png" height="450" >}}
+
+6.  Now you can drop and drag the files between your personal computer
+    and the HCC supercomputers.   
+    {{< figure src="/images/3178539.png" height="450" >}}
+
+
+