added template

AUTHORS

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+FIXME: list authors' names and email addresses.

CITATION

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+FIXME: describe how to cite this lesson.

CONTRIBUTING.md

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+# Contributing
+
+[Software Carpentry][swc-site] and [Data Carpentry][dc-site] are open source projects,
+and we welcome contributions of all kinds:
+new lessons,
+fixes to existing material,
+bug reports,
+and reviews of proposed changes are all welcome.
+
+## Contributor Agreement
+
+By contributing,
+you agree that we may redistribute your work under [our license](LICENSE.md).
+In exchange,
+we will address your issues and/or assess your change proposal as promptly as we can,
+and help you become a member of our community.
+Everyone involved in [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
+agrees to abide by our [code of conduct](CONDUCT.md).
+
+## How to Contribute
+
+The easiest way to get started is to file an issue
+to tell us about a spelling mistake,
+some awkward wording,
+or a factual error.
+This is a good way to introduce yourself
+and to meet some of our community members.
+
+1.  If you do not have a [GitHub][github] account,
+    you can [send us comments by email][contact].
+    However,
+    we will be able to respond more quickly if you use one of the other methods described below.
+
+2.  If you have a [GitHub][github] account,
+    or are willing to [create one][github-join],
+    but do not know how to use Git,
+    you can report problems or suggest improvements by [creating an issue][issues].
+    This allows us to assign the item to someone
+    and to respond to it in a threaded discussion.
+
+3.  If you are comfortable with Git,
+    and would like to add or change material,
+    you can submit a pull request (PR).
+    Instructions for doing this are [included below](#using-github).
+
+## Where to Contribute
+
+1.  If you wish to change this lesson,
+    please work in <https://github.com/swcarpentry/FIXME>,
+    which can be viewed at <https://swcarpentry.github.io/FIXME>.
+
+2.  If you wish to change the example lesson,
+    please work in <https://github.com/swcarpentry/lesson-example>,
+    which documents the format of our lessons
+    and can be viewed at <https://swcarpentry.github.io/lesson-example>.
+
+3.  If you wish to change the template used for workshop websites,
+    please work in <https://github.com/swcarpentry/workshop-template>.
+    The home page of that repository explains how to set up workshop websites,
+    while the extra pages in <https://swcarpentry.github.io/workshop-template>
+    provide more background on our design choices.
+
+4.  If you wish to change CSS style files, tools,
+    or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
+    please work in <https://github.com/swcarpentry/styles>.
+
+## What to Contribute
+
+There are many ways to contribute,
+from writing new exercises and improving existing ones
+to updating or filling in the documentation
+and and submitting [bug reports][issues]
+about things that don't work, aren't clear, or are missing.
+If you are looking for ideas,
+please see [the list of issues for this repository][issues],
+or the issues for [Data Carpentry][dc-issues]
+and [Software Carpentry][swc-issues] projects.
+
+Comments on issues and reviews of pull requests are just as welcome:
+we are smarter together than we are on our own.
+Reviews from novices and newcomers are particularly valuable:
+it's easy for people who have been using these lessons for a while
+to forget how impenetrable some of this material can be,
+so fresh eyes are always welcome.
+
+## What *Not* to Contribute
+
+Our lessons already contain more material than we can cover in a typical workshop,
+so we are usually *not* looking for more concepts or tools to add to them.
+As a rule,
+if you want to introduce a new idea,
+you must (a) estimate how long it will take to teach
+and (b) explain what you would take out to make room for it.
+The first encourages contributors to be honest about requirements;
+the second, to think hard about priorities.
+
+We are also not looking for exercises or other material that only run on one platform.
+Our workshops typically contain a mixture of Windows, Mac OS X, and Linux users;
+in order to be usable,
+our lessons must run equally well on all three.
+
+## Using GitHub
+
+If you choose to contribute via GitHub,
+you may want to look at
+[How to Contribute to an Open Source Project on GitHub][how-contribute].
+In brief:
+
+1.  The published copy of the lesson is in the `gh-pages` branch of the repository
+    (so that GitHub will regenerate it automatically).
+    Please create all branches from that,
+    and merge the [master repository][repo]'s `gh-pages` branch into your `gh-pages` branch
+    before starting work.
+    Please do *not* work directly in your `gh-pages` branch,
+    since that will make it difficult for you to work on other contributions.
+
+2.  We use [GitHub flow][github-flow] to manage changes:
+    1.  Create a new branch in your desktop copy of this repository for each significant change.
+    2.  Commit the change in that branch.
+    3.  Push that branch to your fork of this repository on GitHub.
+    4.  Submit a pull request from that branch to the [master repository][repo].
+    5.  If you receive feedback,
+        make changes on your desktop and push to your branch on GitHub:
+        the pull request will update automatically.
+
+Each lesson has two maintainers who review issues and pull requests
+or encourage others to do so.
+The maintainers are community volunteers,
+and have final say over what gets merged into the lesson.
+
+## Other Resources
+
+General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
+happens on the [discussion mailing list][discuss-list],
+which everyone is welcome to join.
+You can also [reach us by email][contact].
+
+[contact]: mailto:[email protected]
+[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
+[dc-lessons]: http://datacarpentry.org/lessons/
+[dc-site]: http://datacarpentry.org/
+[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
+[github]: http://github.com
+[github-flow]: https://guides.github.com/introduction/flow/
+[github-join]: https://github.com/join
+[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
+[issues]: https://github.com/swcarpentry/FIXME/issues/
+[repo]: https://github.com/swcarpentry/FIXME/
+[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
+[swc-lessons]: http://software-carpentry.org/lessons/
+[swc-site]: http://software-carpentry.org/

_config.yml

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+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this ("swc", "dc", or "lc")?
+carpentry: "dc"
+
+# Overall title for pages.
+title: "Genomics Organization"
+
+# Contact.  This *must* include the protocol: if it's an email
+# address, it must look like "mailto:[email protected]",
+# or if it's a URL, "https://gitter.im/username/ProjectName".
+contact: "mailto:[email protected]"
+
+#------------------------------------------------------------
+# Generic settings (should not need to change).
+#------------------------------------------------------------
+
+# What kind of thing is this ("workshop" or "lesson")?
+kind: "lesson"
+
+# Magic to make URLs resolve both locally and on GitHub.
+# See https://help.github.com/articles/repository-metadata-on-github-pages/.
+repository: <USERNAME>/<PROJECT>
+
+# Sites.
+amy_site: "https://amy.software-carpentry.org/workshops"
+dc_site: "http://datacarpentry.org"
+swc_github: "https://github.com/swcarpentry"
+swc_site: "https://software-carpentry.org"
+swc_pages: "https://swcarpentry.github.io"
+lc_site: "http://librarycarpentry.github.io/"
+template_repo: "https://github.com/swcarpentry/styles"
+example_repo: "https://github.com/swcarpentry/lesson-example"
+example_site: "https://swcarpentry.github.com/lesson-example"
+workshop_repo: "https://github.com/swcarpentry/workshop-template"
+workshop_site: "https://swcarpentry.github.io/workshop-template"
+training_site: "https://swcarpentry.github.io/instructor-training"
+
+# Surveys.
+pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
+post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
+training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training"
+
+# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
+start_time: 0
+
+# Specify that things in the episodes collection should be output.
+collections:
+  episodes:
+    output: true
+    permalink: /:path/
+  extras:
+    output: true
+
+# Set the default layout for things in the episodes collection.
+defaults:
+  - values:
+      root: ..
+  - scope:
+      path: ""
+      type: episodes
+    values:
+      layout: episode
+
+# Files and directories that are not to be copied.
+exclude:
+  - Makefile
+  - bin
+
+# Turn off built-in syntax highlighting.
+highlighter: false

_episodes/01-introduction.md

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+---
+title: "Introduction"
+teaching: 0
+exercises: 0
+questions:
+- "Key question"
+objectives:
+- "First objective."
+keypoints:
+- "First key point."
+---

_extras/about.md

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+---
+layout: page
+title: About
+permalink: /about/
+---
+{% include carpentries.html %}

_extras/discuss.md

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+---
+layout: page
+title: Discussion
+permalink: /discuss/
+---
+FIXME

_extras/figures.md

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+---
+layout: page
+title: Figures
+permalink: /figures/
+---
+{% include all_figures.html %}

_extras/guide.md

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+---
+layout: page
+title: "Instructor Notes"
+permalink: /guide/
+---
+FIXME

_includes/all_figures.html

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+<!-- empty -->

aio.md

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+---
+layout: page 
+permalink: /aio/
+---
+<script>
+  window.onload = function() {
+    var lesson_episodes = [
+    {% for episode in site.episodes %}
+    "{{ episode.url}}"{% unless forloop.last %},{% endunless %}
+    {% endfor %}
+    ];
+    var xmlHttp = [];  /* Required since we are going to query every episode. */
+    for (i=0; i < lesson_episodes.length; i++) {
+      xmlHttp[i] = new XMLHttpRequest();
+      xmlHttp[i].episode = lesson_episodes[i];  /* To enable use this later. */
+      xmlHttp[i].onreadystatechange = function() {
+      if (this.readyState == 4 && this.status == 200) {
+        var article_here = document.getElementById(this.episode);
+        var parser = new DOMParser();
+        var htmlDoc = parser.parseFromString(this.responseText,"text/html");
+        var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
+        article_here.innerHTML = htmlDocArticle.innerHTML;
+        }
+      }
+      episode_url = "{{ page.root }}" + lesson_episodes[i];
+      xmlHttp[i].open("GET", episode_url);
+      xmlHttp[i].send(null);
+    }
+  }
+</script>
+{% comment %}
+Create anchor for each one of the episodes.
+{% endcomment %}
+{% for episode in site.episodes %}
+<article id="{{ episode.url }}"></article>
+{% endfor %}

index.md

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+---
+layout: lesson
+root: .
+---
+FIXME: home page introduction
+
+> ## Prerequisites
+>
+> FIXME
+{: .prereq}

reference.md

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+---
+layout: reference
+permalink: /reference/
+---
+
+## Glossary
+
+FIXME

setup.md

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+---
+layout: page
+title: Setup
+permalink: /setup/
+---
+FIXME