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Commit 17f6d521 authored by Carrie A Brown's avatar Carrie A Brown
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Merge branch '2017attachments' into 'master' 

2017attachments

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content/events/2017/hcc_users_group.md
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......@@ -12,15 +12,5 @@ March 17th 2017: HCCGo by Derek Weitzel
### Avery 108 3 to 4 pm
[Speaker Slides](attachments/17043472/17043471.pdf)
 
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[HCCGo-3-17-17.pdf](attachments/17043472/17043471.pdf)
(application/pdf)
[Speaker Slides](https://unl.box.com/s/404y4itj0i5f251d0gzg3sy1ul73sttx)
content/events/2017/hgrlab_anvil_presentation.md
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......@@ -8,16 +8,5 @@ Meeting: 07/25/2017
Time: 3pm
Presentation
slides: [hgrlab\_anvil.pdf](attachments/21070371/21070533.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[hgrlab\_anvil.pdf](attachments/21070371/21070373.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[hgrlab\_anvil.pdf](attachments/21070371/21070533.pdf)
(application/pdf)
slides: [hgrlab\_anvil.pdf](https://unl.box.com/s/37j1r8p6vhagdinge2r4ti5vpwgo3tlr)
content/events/2017/june_workshop_series_2017.md
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......@@ -3,7 +3,7 @@ title = "June Workshop Series 2017"
description = "June Workshop Series 2017."
+++
<a href="https://hcc.unl.edu/june-workshop-series" class="external-link">https://hcc.unl.edu/june-workshop-series</a>
[Series Website](https://hcc.unl.edu/june-workshop-series)
=====================================================================================================================
**June 6th and 13th: Bash and Git**
......@@ -18,11 +18,8 @@ Carpentry lessons.
#### Workshop Materials:
- Links to Lessons:
<a href="https://unlhcc.github.io/2017-06-06-UNL/" class="external-link">https://unlhcc.github.io/2017-06-06-UNL/</a>
- Attendee Portal:
<a href="http://hcc.unl.edu/swc-history/index.html" class="external-link">http://hcc.unl.edu/swc-history/index.html</a>
- [Lessons](https://unlhcc.github.io/2017-06-06-UNL/)
- [Attendee Portal](http://hcc.unl.edu/swc-history/index.html)
**June 20th: Introductory HCC**
===============================
......@@ -34,11 +31,8 @@ handling data and tips on how to optimize workflow.
#### Workshop Materials:
- Presenter Slides:
- [Introduction to HCC.pptx](attachments/18548621/18548623.pptx)
- [Introduction to HCC.pdf](attachments/18548621/18548624.pdf)
- Etherpad:
<a href="https://etherpad.wikimedia.org/p/2017_06_20_UNL" class="external-link">https://etherpad.wikimedia.org/p/2017_06_20_UNL</a>
- [Introduction to HCC.pptx](https://unl.box.com/s/80j5ke5busbbwrh7aw4rdndf1x5rengj)
- [Introduction to HCC.pdf](https://unl.box.com/s/xzx5koenk9u8rf2ervzq35mp7qz8s9mx)
**June 27th: All about SLURM**
==============================
......@@ -50,36 +44,6 @@ options to streamline your jobs.
#### Workshop Materials:
- Presenter Slides:
- [All About Slurm.pptx](attachments/18548621/18549050.pptx)
- [All About Slurm.pdf](attachments/18548621/21070067.pdf)
- Etherpad:
<a href="https://etherpad.wikimedia.org/p/2017_06_27_UNL" class="external-link">https://etherpad.wikimedia.org/p/2017_06_27_UNL</a>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Introduction to HCC 2.pptx](attachments/18548621/18548623.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Introduction to HCC.pdf](attachments/18548621/18548624.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
About Slurm.pdf](attachments/18548621/21070066.pdf) (application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
About Slurm.pptx](attachments/18548621/21070065.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
About Slurm.pptx](attachments/18548621/18549050.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
About Slurm.pdf](attachments/18548621/18549049.pdf) (application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [All
About Slurm pdf.pdf](attachments/18548621/21070067.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Intro
to HCC.pdf](attachments/18548621/33686225.pdf) (application/pdf)
- [All About Slurm.pptx](https://unl.box.com/s/yv6j003n3u5kgh3qw93v2hvgwoihvjbh)
- [All About Slurm.pdf](https://unl.box.com/s/wn1dfbd5tkyc8fo40z5rl8m9if8kfhe6)
content/events/2017/software_carpentry_workshop_unl_january_5_6_2017.md deleted 100644 → 0
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+++
title = "SWC Workshop, Jan. 5-6 2017"
description = "SWC Workshop, Jan. 5-6 2017."
+++
**When**: January 5-6, 2017
**Where**: Jackie Gaughan Multicultural Center - room 202 (Ubuntu)
**Quick Link**:
<a href="https://eharstad.github.io/2017-01-05-UNL" class="external-link">https://eharstad.github.io/2017-01-05-UNL</a>
**Materials**
=============
**Introduction:**
**<span
class="confluence-embedded-file-wrapper"><a href="/download/attachments/17041001/SWC-UNL-2017_01_05.pptx?version=1&amp;modificationDate=1483674264000&amp;api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/17041003/1" height="250" /></a></span>**
**<span
class="confluence-embedded-file-wrapper"><a href="/download/attachments/17041001/SWC-UNL-2017_01_05.pdf?version=1&amp;modificationDate=1483674263000&amp;api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/17041002/1" height="250" /></a></span>
**
**Etherpad**:
<a href="https://public.etherpad-mozilla.org/p/2017-01-05-UNL" class="external-link">https://public.etherpad-mozilla.org/p/2017-01-05-UNL</a>
**Shell Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/shell-novice/" class="external-link">https://eharstad.github.io/shell-novice/</a>
**Git Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
**R Lesson**:<span
style="color: rgb(24,54,145);"> </span><a href="https://carriebrown.github.io/r-novice-gapminder/" class="external-link">https://carriebrown.github.io/r-novice-gapminder/</a>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pdf](attachments/17041001/17041002.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pptx](attachments/17041001/17041003.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
content/events/2017/software_carpentry_workshop_unl_march_27_28_2017.md deleted 100644 → 0
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+++
title = "SWC Workshop, March 27-28, 2017"
description = "SWC Workshop, March 27-28, 2017."
+++
**When**: March 27-28, 2017
**Where**: Nebraska Union - Colonial A&B
**Quick Link**:
<a href="https://unlhcc.github.io/2017-03-27-UNL/" class="external-link">https://unlhcc.github.io/2017-03-27-UNL/</a>
**Materials**
=============
**
**
**
**
**
**
**Etherpad**:
<a href="http://pad.software-carpentry.org/2017_03_27_UNL" class="external-link">http://pad.software-carpentry.org/2017_03_27_UNL</a>
**Intro
Slides: [SWC-UNL-20170327.pdf](attachments/17043687/17043692.pdf)**
**Shell Log:**
<a href="http://hcc.unl.edu/swc-history/20170327.html" class="external-link">http://hcc.unl.edu/swc-history/20170327.html</a>
**Shell Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/shell-novice/" class="external-link">https://eharstad.github.io/shell-novice/</a>
**Git Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
**Python Lesson**:<span
style="color: rgb(24,54,145);"> </span><a href="https://djw8605.github.io/python-novice-inflammation/" class="external-link">https://djw8605.github.io/python-novice-inflammation/</a>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pptx](attachments/17043687/17043685.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pdf](attachments/17043687/17043686.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-20170327.pdf](attachments/17043687/17043692.pdf)
(application/pdf)
content/events/2017/unk_linear_algebra_feb_28th_2017.md
View file @ 17f6d521
......@@ -12,11 +12,10 @@ top of your monitor and a helper will be around to assist you.**
**What is a cluster:**
----------------------
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042191.png" class="confluence-embedded-image" width="700" height="307" /></span>
![cluster image](/images/cluster_small.png)
(picture courtesy of:
<a href="http://training.h3abionet.org/technical_workshop_2015/?page_id=403" class="external-link">http://training.h3abionet.org/technical_workshop_2015/?page_id=403</a>)
[http://training.h3abionet.org/technical_workshop_2015/?page_id=403](http://training.h3abionet.org/technical_workshop_2015/?page_id=403))
**
**
......@@ -28,182 +27,25 @@ class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img sr
small green light in the middle of the Yubikey to indicate it is
inserted correctly.
- Open your preferred web browser and navigate to
<a href="http://go.unl.edu/cranessh" class="external-link">http://go.unl.edu/cranessh</a>
[http://go.unl.edu/cranessh](http://go.unl.edu/cranessh)
- Click "Start SSH session to crane.unl.edu"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042178.png" class="confluence-embedded-image" height="400" /></span>
![](/images/ssh.png)
- Click the "Terminal: SSH" icon to begin the SSH session
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042179.png" class="confluence-embedded-image" height="400" /></span>
![](/images/terminalSSH.png)
- Type in the provided Username and Password. Note that the password
will not display on screen, but rest assured that even though
nothing is being output, your password is being entered as you type.
- At the "Passcode:" prompt, press your finger to the gold circle in
the middle of the Yubikey until a string of characters appears on
screen.
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042182.png" class="confluence-embedded-image" height="400" /></span>
![](/images/yubikey.png)
- If you logged in successfully, your screen should look similar to
the one belo
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042183.png" class="confluence-embedded-image" height="400" /></span>
![](/images/crane_login.png)
**Linux Commands Reference List:**
----------------------------------
<table>
<colgroup>
<col style="width: 33%" />
<col style="width: 33%" />
<col style="width: 33%" />
</colgroup>
<thead>
<tr class="header">
<th>Command</th>
<th>What it does</th>
<th>Example Uses</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>ls</td>
<td>list: Lists the files and directories located in the current directory</td>
<td><ul>
<li>ls</li>
<li>ls -a
<ul>
<li>shows all the files in the directory, including hidden ones</li>
</ul></li>
<li>ls -l
<ul>
<li>shows contents in a list format including information such as file size, file permissions and date the file was modified</li>
</ul></li>
<li>ls *.txt
<ul>
<li>shows all files in the current directory which end with .txt</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>cd</td>
<td>change directory: this allows users to in or out of file directories</td>
<td><ul>
<li>cd &lt;folder path&gt;</li>
<li>cd folder_name
<ul>
<li>navigates into directory &quot;folder_name&quot; located in the current directory</li>
</ul></li>
<li>cd ..
<ul>
<li>navigates out of a directory and into the parent directory</li>
</ul>
cd $HOME (or $WORK)
<ul>
<li>navigates to a user's home (or work) directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>mv</td>
<td>move: used to move a file or directory to another location</td>
<td><ul>
<li>mv &lt;current file(s)&gt; &lt;target file(s)&gt;</li>
<li>mv * ../
<ul>
<li>moves all files from the current directory into the parent directory</li>
</ul></li>
<li>mv old_filename new_filename
<ul>
<li>renames the file &quot;old_filename&quot; to &quot;new_filename&quot;</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>man</td>
<td><p>manual: displays documentation for commands</p>
<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the manual display, press 'q'</p></td>
<td><ul>
<li>man &lt;command name&gt;</li>
<li>man ls
<ul>
<li>displays documentation for the ls command</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>mkdir</td>
<td>make directory: creates a directory with the specified name</td>
<td><ul>
<li>mkdir &lt;new_folder&gt;
<ul>
<li>creates the directory &quot;new_folder&quot; within the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>rmdir</td>
<td><p>remove directory: deletes a directory with the specified name</p>
<p><strong>Note:</strong> rmdir only works on empty directories</p></td>
<td><ul>
<li>rmdir &lt;folder_name&gt;
<ul>
<li>removes the directory &quot;folder_name&quot; if the directory</li>
</ul></li>
<li>rmdir *
<ul>
<li>removes all directories within the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>rm</td>
<td>remove: deletes file or files with the specified name(s)</td>
<td><ul>
<li>rm &lt;file_name&gt;
<ul>
<li>deletes the file &quot;file_name&quot;</li>
</ul></li>
<li>rm *
<ul>
<li>deletes all files in the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td><p>nano</p></td>
<td><p>nano text editor: opens the nano text editor</p>
<p><strong>Note:</strong> To access the menu options, ^ indicates the control (CTRL) key.</p></td>
<td><ul>
<li>nano
<ul>
<li>opens the text editor in a blank file</li>
</ul></li>
<li>nano &lt;file_name&gt;
<ul>
<li>opens the text editor with &quot;file_name&quot; open. If &quot;file_name&quot; does not exist, it will be created if the file is saved</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>clear</td>
<td>clear: clears the screen of all input/output</td>
<td><ul>
<li>clear</li>
</ul></td>
</tr>
<tr class="even">
<td>less</td>
<td><p>less: opens an extended view of a file</p>
<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the extended view, press 'q'</p></td>
<td><ul>
<li>less &lt;file_name&gt;
<ul>
<li>opens an extended view of the file &quot;file_name&quot;</li>
</ul></li>
</ul></td>
</tr>
</tbody>
</table>
https://hcc.unl.edu/docs/quickstarts/connecting/basic_linux_commands/
**To run MATLAB interactively:**
--------------------------------
......@@ -228,35 +70,3 @@ cd $HOME (or $WORK)
- Clone the github repo containing the tutorial files:
- git clone https://github.com/unlhcc/HCCWorkshops.git
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.31 PM.png](attachments/17042185/17042180.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.43 PM.png](attachments/17042185/17042181.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.31 PM.png](attachments/17042185/17042178.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.43 PM.png](attachments/17042185/17042179.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.16.10 PM.png](attachments/17042185/17042182.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.16.37 PM.png](attachments/17042185/17042184.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.16.37 PM.png](attachments/17042185/17042183.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2017-2-24 11:14:4.png](attachments/17042185/17042186.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[cluster\_small2.png](attachments/17042185/17042191.png) (image/png)
content/events/2017/unl_r_for_biologists_class_march_8_2017.md
View file @ 17f6d521
......@@ -14,7 +14,7 @@ note to the back of your computer screen and a helper will assist you.**
If you have not already requested an HCC account under the rcourse998
group, please do so
here: <a href="https://hcc.unl.edu/new-user-request" class="external-link">https://hcc.unl.edu/new-user-request</a>
[here](https://hcc.unl.edu/new-user-request)
If you already have an HCC account and need to be added to the
rcourse998 group, please let us know.
......@@ -32,29 +32,35 @@ For Windows will we use two third party
application **PuTTY** and **WinSCP** for demonstration.
PuTTY:  
&lt;[putty-0.62-installer.exe](https://hcc-docs.unl.edu/download/attachments/2851288/putty-0.62-installer.exe?version=1&modificationDate=1371067913000&api=v2) or <a href="http://www.putty.org/" class="external-link">http://www.putty.org/</a>&gt;
&lt;[http://www.putty.org/](http://www.putty.org/)&gt;
WinSCP:
&lt;[winscp515setup.exe](https://hcc-docs.unl.edu/download/attachments/2851288/winscp515setup.exe?version=1&modificationDate=1371155133000&api=v2) or <a href="http://winscp.net/eng/download.php" class="external-link">http://winscp.net/eng/download.php</a>&gt;. 
&lt; [http://winscp.net/eng/download.php](http://winscp.net/eng/download.php)&gt;
**Mac/Linux:**
Mac and Linux users will need to download and install **Cyberduck**.
Detailed information for downloading and setting up Cyberduck can be
found here: [For Mac/Linux Users](2851290.html)
found here: [For Mac/Linux Users](https://cyberduck.io/)
 
**R core and R Studio:**
**Linux Commands Reference List:**
[https://hcc.unl.edu/docs/quickstarts/connecting/basic_linux_commands/](https://hcc.unl.edu/docs/quickstarts/connecting/basic_linux_commands/)
 
**R core and R Studio:**
We will be writing scripts offline in RStudio and then uploading them to
execute them on the cluster. This lesson assumes you have the R core and
RStudio installed. If you do not you can install them here:
R
core: <a href="https://cloud.r-project.org/" class="external-link">https://cloud.r-project.org/</a>
core: [https://cloud.r-project.org/](https://cloud.r-project.org/)
RStudio: <a href="https://www.rstudio.com/products/rstudio/download/" class="external-link">https://www.rstudio.com/products/rstudio/download/</a>
RStudio: [https://www.rstudio.com/products/rstudio/download/](https://www.rstudio.com/products/rstudio/download/)
 
......@@ -74,179 +80,10 @@ following commands inside the RStudio console:
**What is a cluster:**
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042692/17042703.png" class="confluence-embedded-image" width="700" height="307" /></span></span>
![](/images/cluster_small.png)
(picture courtesy
of: <a href="http://training.h3abionet.org/technical_workshop_2015/?page_id=403" class="external-link">http://training.h3abionet.org/technical_workshop_2015/?page_id=403</a>)
 
**Linux Commands Reference List:**
----------------------------------
<table>
<colgroup>
<col style="width: 33%" />
<col style="width: 33%" />
<col style="width: 33%" />
</colgroup>
<thead>
<tr class="header">
<th><div class="tablesorter-header-inner">
Command
</div></th>
<th><div class="tablesorter-header-inner">
What it does
</div></th>
<th><div class="tablesorter-header-inner">
Example Uses
</div></th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>ls</td>
<td>list: Lists the files and directories located in the current directory</td>
<td><ul>
<li>ls</li>
<li>ls -a
<ul>
<li>shows all the files in the directory, including hidden ones</li>
</ul></li>
<li>ls -l
<ul>
<li>shows contents in a list format including information such as file size, file permissions and date the file was modified</li>
</ul></li>
<li>ls *.txt
<ul>
<li>shows all files in the current directory which end with .txt</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>cd</td>
<td>change directory: this allows users to in or out of file directories</td>
<td><ul>
<li>cd &lt;folder path&gt;</li>
<li>cd folder_name
<ul>
<li>navigates into directory &quot;folder_name&quot; located in the current directory</li>
</ul></li>
<li>cd ..
<ul>
<li>navigates out of a directory and into the parent directory</li>
</ul>
cd $HOME (or $WORK)
<ul>
<li>navigates to a user's home (or work) directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>mv</td>
<td>move: used to move a file or directory to another location</td>
<td><ul>
<li>mv &lt;current file(s)&gt; &lt;target file(s)&gt;</li>
<li>mv * ../
<ul>
<li>moves all files from the current directory into the parent directory</li>
</ul></li>
<li>mv old_filename new_filename
<ul>
<li>renames the file &quot;old_filename&quot; to &quot;new_filename&quot;</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>man</td>
<td><p>manual: displays documentation for commands</p>
<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the manual display, press 'q'</p></td>