index.html

---
layout: workshop      # DON'T CHANGE THIS.
root: .               # DON'T CHANGE THIS EITHER.  (THANK YOU.)
carpentry: "swc"    # what kind of Carpentry (must be either "dc" or "swc")
venue: "The Jackson Laboratory for Genomic Medicine"        # brief name of host site without address (e.g., "Euphoric State University")
address: "Rooms 2440 & 2445, 10 Discovery Drive, Farmington, Connecticut"      # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria")
country: "us"      # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en"     # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "41.732284, -72.793404"       # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "June 12, 2017"    # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "9:00 am - 5:00 pm"    # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: 2017-06-12      # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: 2017-06-12        # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["Shane Sanders", "Saira Kazmi", "Sandeep Namburi "] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Neil Kindlon", "Aditya Srikanth Kovuri"]     # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: ["susan.mcclatchy@jax.org"]    # boxed, comma-separated list of contact email addresses for the host, lead instructor, or whoever else is handling questions, like ["marlyn.wescoff@example.org", "fran.bilas@example.org", "ruth.lichterman@example.org"]
collaborative_notes: https://public.etherpad-mozilla.org/p/2017-06-12-hpc-farmington            # optional: URL for the workshop collaborative notes, e.g. an Etherpad or Google Docs document
eventbrite: 34255832116          # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
---

<!-- See instructions in the comments below for how to edit specific sections of this workshop template. -->

<!--
  HEADER

  Edit the values in the block above to be appropriate for your workshop.
  If the value is not 'true', 'false', 'null', or a number, please use
  double quotation marks around the value, unless specified otherwise.
  And run 'tools/check' *before* committing to make sure that changes are good.
-->

<!--
  EVENTBRITE

  This block includes the Eventbrite registration widget if
  'eventbrite' has been set in the header.  You can delete it if you
  are not using Eventbrite, or leave it in, since it will not be
  displayed if the 'eventbrite' field in the header is not set.
-->
{% if page.eventbrite %}
<iframe
  src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt"
  frameborder="0"
  width="100%"
  height="288px"
  scrolling="auto">
</iframe>
{% endif %}


<h2 id="general">General Information</h2>

<!--
  INTRODUCTION

  Edit the general explanatory paragraph below if you want to change
  the pitch.
-->
<p>
  <a href="{{site.swc_site}}">Software Carpentry</a>
  aims to help researchers get their work done
  in less time and with less pain
  by teaching them basic research computing skills.
  This hands-on workshop will cover basic concepts and tools,
  including program design, version control, data management,
  and task automation.
  Participants will be encouraged to help one another
  and to apply what they have learned to their own research problems.
</p>
<p align="center">
  <em>
    For more information on what we teach and why,
    please see our paper
    "<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">Best Practices for Scientific Computing</a>".
  </em>
</p>

<!--
  AUDIENCE

  Explain who your audience is.  (In particular, tell readers if the
  workshop is only open to people from a particular institution.
-->
<p id="who">
  <strong>Who:</strong>
  The course is aimed at graduate students and other researchers.
  <strong>You don't need to have any previous knowledge of the tools that will
    be presented at the workshop.</strong>
</p>

<!--
  LOCATION

  This block displays the address and links to maps showing directions
  if the latitude and longitude of the workshop have been set.  You
  can use http://itouchmap.com/latlong.html to find the lat/long of an
  address.
-->
{% if page.latlng %}
<p id="where">
  <strong>Where:</strong>
  {{page.address}}.
  Get directions with
  <a href="//www.openstreetmap.org/?mlat={{page.latlng | replace:',','&mlon='}}&zoom=16">OpenStreetMap</a>
  or
  <a href="//maps.google.com/maps?q={{page.latlng}}">Google Maps</a>.
</p>
{% endif %}

<!--
  DATE

  This block displays the date and links to Google Calendar.
-->
{% if page.humandate %}
<p id="when">
  <strong>When:</strong>
  {{page.humandate}}.
  {% include workshop_calendar.html %}
</p>
{% endif %}

<!--
  SPECIAL REQUIREMENTS

  Modify the block below if there are any special requirements.
-->
<p id="requirements">
  <strong>Requirements:</strong> Participants must bring a laptop with a
  Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges
  on. They should have a few specific software packages installed (listed
  <a href="#setup">below</a>). They are also required to abide by
  Software Carpentry's
  <a href="{{site.swc_site}}/conduct.html">Code of Conduct</a>.
</p>

<!--
  ACCESSIBILITY

  Modify the block below if there are any barriers to accessibility or
  special instructions.
-->
<p id="accessibility">
  <strong>Accessibility:</strong> We are committed to making this workshop
  accessible to everybody.
  The workshop organisers have checked that:
</p>
<ul>
  <li>The room is wheelchair / scooter accessible.</li>
  <li>Accessible restrooms are available.</li>
</ul>
<p>
  Materials will be provided in advance of the workshop and
  large-print handouts are available if needed by notifying the
  organizers in advance.  If we can help making learning easier for
  you (e.g. sign-language interpreters, lactation facilities) please
  <a href="mailto:{{page.contact}}">get in touch</a> and we will
  attempt to provide them.
</p>

<!--
  CONTACT EMAIL ADDRESS

  Display the contact email address set in the configuration file.
-->
<p id="contact">
  <strong>Contact</strong>:
  Please email
  {% if page.contact %}
    {% for contact in page.contact %}
      {% if forloop.last and page.contact.size > 1 %}
        or
      {% else %}
        {% unless forloop.first %}
        ,
        {% endunless %}
      {% endif %}
      <a href='mailto:{{contact}}'>{{contact}}</a>
    {% endfor %}
  {% else %}
    to-be-announced
  {% endif %}
  for more information.
</p>

<hr/>

<!--
  SCHEDULE

  Show the workshop's schedule.  Edit the items and times in the table
  to match your plans.  You may also want to change 'Day 1' and 'Day
  2' to be actual dates or days of the week.
-->
<h2 id="schedule">Schedule</h2>

<!-- DO NOT EDIT SURVEY LINKS -->

<div class="row">
  <div class="col-md-6">
    <h3>Day 1</h3>
    <table class="table table-striped">
      <tr> <td>09:00</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/>Workshop Overview</a></td> </tr>
      <tr> <td>09:15</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/01-intro/>Introducing the Shell</a></td> </tr>
      <tr> <td>09:45</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/02-filedir/>Navigating Files and Directories</a></td> </tr>
      <tr> <td>10:15</td> <td>Coffee</td> </tr>
      <tr> <td>10:30</td> <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/03-create/>Working With Files and Directories</a></td> </tr>
      <tr> <td>11:00</td> <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/04-pipefilter/>Pipes and Filters</a></td> </tr>
      <tr> <td>11:30</td> <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/05-loop/>Loops</a></td> </tr>
      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:00</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/06-script/>Shell Scripts</a></td> </tr>
      <tr> <td>13:30</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/07-find/>Finding Things</a></td> </tr>
      <tr> <td>14:00</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/08-workflow/>Automating a workflow</a></td> </tr>
      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
      <tr> <td>14:45</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/09-hpc_episode_01/>Connecting to clusters (ssh, scp)</a></td> </tr>
      <tr> <td>15:00</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/10-hpc_episode_02/>Queues on HPC</a></td> </tr>
      <tr> <td>15:05</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/11-hpc_episode_03/>Using installed software (modules)</a></td> </tr>
      <tr> <td>15:15</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/12-hpc_episode_04/>Running Jobs on HPC</a></td> </tr>
      <tr> <td>15:30</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/13-hpc_episode_05/>Job Arrays</a></td> </tr>
      <tr> <td>15:45</td>  <td><a href=https://thejacksonlaboratory.github.io/introduction-to-hpc/14-hpc_episode_06/>Writing scripts to submit jobs to the cluster</a></td> </tr>
      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
    </table>
  </div>
</div>

<!--
  Collaborative Notes

  If you want to use an Etherpad, go to

      http://pad.software-carpentry.org/YYYY-MM-DD-site

  where 'YYYY-MM-DD-site' is the identifier for your workshop,
  e.g., '2015-06-10-esu'.
-->
{% if page.collaborative_notes %}
<p id="collaborative_notes">
  We will use this <a href="{{page.collaborative_notes}}">collaborative document</a> for chatting, taking notes, and sharing URLs and bits of code.
</p>
{% endif %}

<hr/>

<!--
  SYLLABUS

  Show what topics will be covered.

  1. If your workshop is R rather than Python, remove the comment
     around that section and put a comment around the Python section.
  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you
     intend to teach.
  4. You may need to move the div's with class="col-md-6" around inside
     the div's with class="row" to balance the multi-column layout.

  This is one of the places where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->
<!--
<h2 id="syllabus">Syllabus</h2>

<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-shell">The Unix Shell</h3>
    <ul>
      <li>Files and directories</li>
      <li>History and tab completion</li>
      <li>Pipes and redirection</li>
      <li>Looping over files</li>
      <li>Creating and running shell scripts</li>
      <li>Finding things</li>
      <li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
    </ul>
  </div>
     
<div class="col-md-6">
    <h3 id="syllabus-python">Programming in Python</h3>
    <ul>
      <li>Using libraries</li>
      <li>Working with arrays</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Defensive programming</li>
      <li>Using Python from the command line</li>
      <li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
    </ul>
  </div>

  <div class="col-md-6">
    <h3 id="syllabus-r">Programming in R</h3>
    <ul>
      <li>Working with vectors and data frames</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Using R from the command line</li>
      <li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
    </ul>
  </div>
  -->
  <!--
  <div class="col-md-6">
    <h3 id="syllabus-matlab">Programming in MATLAB</h3>
    <ul>
      <li>Working with arrays</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Defensive programming</li>
      <li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
     </ul>
   </div>
  
</div>

<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-git">Version Control with Git</h3>
    <ul>
      <li>Creating a repository</li>
      <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
      <li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
      <li>Ignoring files</li>
      <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
      <li>Resolving conflicts</li>
      <li>Open licenses</li>
      <li>Where to host work, and why</li>
      <li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3 id="syllabus-sql">Managing Data with SQL</h3>
    <ul>
      <li>Reading and sorting data</li>
      <li>Filtering with <code>where</code></li>
      <li>Calculating new values on the fly</li>
      <li>Handling missing values</li>
      <li>Combining values using aggregation</li>
      <li>Combining information from multiple tables using <code>join</code></li>
      <li>Creating, modifying, and deleting data</li>
      <li>Programming with databases</li>
      <li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
    </ul>
  </div>
</div>

<hr/>
 -->
<!--
  SETUP

  Delete irrelevant sections from the setup instructions.  Each
  section is inside a 'div' without any classes to make the beginning
  and end easier to find.

  This is the other place where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->

<h2 id="setup">Setup</h2>

<p>
  To participate in a Software Carpentry workshop, you will need
  access to the software described below. In addition, you will
  need an up-to-date web browser.
</p>
<p>
  We maintain a list of common issues that occur during installation as a reference for instructors
  that may be useful on the
  <a href = "{{site.swc_github}}/workshop-template/wiki/Configuration-Problems-and-Solutions">Configuration Problems and Solutions wiki page</a>.
</p>

<div id="shell"> <!-- Start of 'shell' section. -->
  <h3>The Bash Shell</h3>

  <p>
    Bash is a commonly-used shell that gives you the power to do simple
    tasks more quickly.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="shell-windows">Windows</h4>
      <a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
      <ol>
        <li>Download the Git for Windows <a href="https://git-for-windows.github.io/">installer</a>.</li>
        <li>Run the installer and follow the steps bellow:
          <ol>
            <!-- Git 2.8.2 Setup -->
            <!-- Information -->
            <li>Click on "Next".</li>
            <!-- Select Components -->
            <li>Click on "Next".</li>
            <!-- Adjusting your PATH environment -->
            <li>
              <strong>
                Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
              </strong>
                If you forgot to do this programs that you need for the workshop will not work properly.
                If this happens rerun the installer and select the appropriate option.
            </li>
            <!-- Choosing the SSH executable -->
            <li>Click on "Next".</li>
            <!-- Configuring the line ending conversions -->
            <li>
              <strong>
                Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
              </strong>
            </li>
            <!-- Configuring the terminal emulator to use with Git Bash -->
            <li>
              <strong>
                Keep "Use Windows' default console window" selected and click on "Next".
              </strong>
            </li>
            <!-- Configuring experimental performance tweaks -->
            <li>Click on "Install".</li>
            <!-- Installing -->
            <!-- Completing the Git Setup Wizard -->
            <li>Click on "Finish".</li>
          </ol>
        </li>
        <li>
          If your "HOME" environment variable is not set (or you don't know what this is):
          <ol>
            <li>Open command prompt (Open Start Menu then type <code>cmd</code> and press [Enter])</li>
            <li>
              Type the following line into the command prompt window exactly as shown:
              <p><code>setx HOME "%USERPROFILE%"</code></p>
            </li>
            <li>Press [Enter], you should see <code>SUCCESS: Specified value was saved.</code></li>
            <li>Quit command prompt by typing <code>exit</code> then pressing [Enter]</li>
          </ol>
        </li>
      </ol>
      <p>This will provide you with both Git and Bash in the Git Bash program.</p>
    </div>
    <div class="col-md-4">
      <h4 id="shell-macosx">Mac OS X</h4>
      <p>
        The default shell in all versions of Mac OS X is Bash, so no
        need to install anything.  You access Bash from the Terminal
        (found in
        <code>/Applications/Utilities</code>).
        See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
        for an example on how to open the Terminal.
        You may want to keep
        Terminal in your dock for this workshop.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="shell-linux">Linux</h4>
      <p>
        The default shell is usually Bash, but if your
        machine is set up differently you can run it by opening a
        terminal and typing <code>bash</code>.  There is no need to
        install anything.
      </p>
    </div>
  </div>
</div> <!-- End of 'shell' section. -->

<div id="editor"> <!-- Start of 'editor' section. -->
  <h3>Text Editor</h3>

  <p>
    When you're writing code, it's nice to have a text editor that is
    optimized for writing code, with features like automatic
    color-coding of key words.  The default text editor on Mac OS X and
    Linux is usually set to Vim, which is not famous for being
    intuitive.  if you accidentally find yourself stuck in it, try
    typing the escape key, followed by <code>:q!</code> (colon, lower-case 'q',
    exclamation mark), then hitting Return to return to the shell.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="editor-windows">Windows</h4>
      <a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
      <p>
        nano is a basic editor and the default that instructors use in the workshop.
        To install it,
        download the <a href="{{site.swc_installer}}">Software Carpentry Windows installer</a>
        and double click on the file to run it.
        <strong>This installer requires an active internet connection.</strong>
      </p>
      <p>
        Others editors that you can use are
        <a href="http://notepad-plus-plus.org/">Notepad++</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
        <strong>Be aware that you must
          add its installation directory to your system path.</strong>
        Please ask your instructor to help you do this.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="editor-macosx">Mac OS X</h4>
      <p>
        nano is a basic editor and the default that instructors use in the workshop.
        See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
        for an example on how to open nano.
        It should be pre-installed.
      </p>
      <p>
        Others editors that you can use are
        <a href="http://www.barebones.com/products/textwrangler/">Text Wrangler</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="editor-linux">Linux</h4>
      <p>
        nano is a basic editor and the default that instructors use in the workshop.
        It should be pre-installed.
      </p>
      <p>
        Others editors that you can use are
        <a href="https://wiki.gnome.org/Apps/Gedit">Gedit</a>,
        <a href="http://kate-editor.org/">Kate</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
      </p>
    </div>
  </div>
</div> <!-- End of 'editor' section. -->
<div id="vm">
  <h3>SSH and SCP (Putty and WinScp) - Call helpdesk for help with this software.</h3>
  <p>
    For windows machines, you will need Putty to be able to connect to the hpc nodes.  
  </p>
  <ol>
    <li>
      For secure shell (ssh), download and install <a href="http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html">Putty</a>.
    </li>
    <li>
       For secure file copy (scp), download and install <a href="http://winscp.net/eng/download.php">WinSCP</a>.
    </li>
  </ol>
</div>