diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 00000000..659aeece --- /dev/null +++ b/AUTHORS @@ -0,0 +1 @@ +FIXME: list authors' names and email addresses. diff --git a/CITATION b/CITATION new file mode 100644 index 00000000..d5bfc2b3 --- /dev/null +++ b/CITATION @@ -0,0 +1 @@ +FIXME: describe how to cite this lesson. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..9de5a12a --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,151 @@ +# 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 , + which can be viewed at . + +2. If you wish to change the example lesson, + please work in , + which documents the format of our lessons + and can be viewed at . + +3. If you wish to change the template used for workshop websites, + please work in . + The home page of that repository explains how to set up workshop websites, + while the extra pages in + 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 . + +## 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:admin@software-carpentry.org +[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/ diff --git a/_config.yml b/_config.yml new file mode 100644 index 00000000..273a661a --- /dev/null +++ b/_config.yml @@ -0,0 +1,73 @@ +#------------------------------------------------------------ +# 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:lessons@software-carpentry.org", +# or if it's a URL, "https://gitter.im/username/ProjectName". +contact: "mailto:lessons@software-carpentry.org" + +#------------------------------------------------------------ +# 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: / + +# 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 diff --git a/_episodes/01-introduction.md b/_episodes/01-introduction.md new file mode 100644 index 00000000..4f375b3b --- /dev/null +++ b/_episodes/01-introduction.md @@ -0,0 +1,11 @@ +--- +title: "Introduction" +teaching: 0 +exercises: 0 +questions: +- "Key question" +objectives: +- "First objective." +keypoints: +- "First key point." +--- diff --git a/_extras/about.md b/_extras/about.md new file mode 100644 index 00000000..aa7beea3 --- /dev/null +++ b/_extras/about.md @@ -0,0 +1,6 @@ +--- +layout: page +title: About +permalink: /about/ +--- +{% include carpentries.html %} diff --git a/_extras/discuss.md b/_extras/discuss.md new file mode 100644 index 00000000..1d467a48 --- /dev/null +++ b/_extras/discuss.md @@ -0,0 +1,6 @@ +--- +layout: page +title: Discussion +permalink: /discuss/ +--- +FIXME diff --git a/_extras/figures.md b/_extras/figures.md new file mode 100644 index 00000000..de99a578 --- /dev/null +++ b/_extras/figures.md @@ -0,0 +1,6 @@ +--- +layout: page +title: Figures +permalink: /figures/ +--- +{% include all_figures.html %} diff --git a/_extras/guide.md b/_extras/guide.md new file mode 100644 index 00000000..0bad9951 --- /dev/null +++ b/_extras/guide.md @@ -0,0 +1,6 @@ +--- +layout: page +title: "Instructor Notes" +permalink: /guide/ +--- +FIXME diff --git a/_includes/all_figures.html b/_includes/all_figures.html new file mode 100644 index 00000000..c341a403 --- /dev/null +++ b/_includes/all_figures.html @@ -0,0 +1 @@ + diff --git a/aio.md b/aio.md new file mode 100644 index 00000000..6d938523 --- /dev/null +++ b/aio.md @@ -0,0 +1,36 @@ +--- +layout: page +permalink: /aio/ +--- + +{% comment %} +Create anchor for each one of the episodes. +{% endcomment %} +{% for episode in site.episodes %} +
+{% endfor %} diff --git a/index.md b/index.md new file mode 100644 index 00000000..e2fcde36 --- /dev/null +++ b/index.md @@ -0,0 +1,10 @@ +--- +layout: lesson +root: . +--- +FIXME: home page introduction + +> ## Prerequisites +> +> FIXME +{: .prereq} diff --git a/reference.md b/reference.md new file mode 100644 index 00000000..87a20cca --- /dev/null +++ b/reference.md @@ -0,0 +1,8 @@ +--- +layout: reference +permalink: /reference/ +--- + +## Glossary + +FIXME diff --git a/setup.md b/setup.md new file mode 100644 index 00000000..2dc2e460 --- /dev/null +++ b/setup.md @@ -0,0 +1,6 @@ +--- +layout: page +title: Setup +permalink: /setup/ +--- +FIXME