Merge branch 'gh-pages' into metadata_episode

Toby Hodges · Toby Hodges · commit 7560f43b2197 · 2017-08-07T11:04:47.000+02:00
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -1,9 +0,0 @@
-Please delete the text below before submitting your contribution. 
-
----
-
-Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
-
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  
-
----
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,9 +0,0 @@
-Please delete the text below before submitting your contribution. 
-
----
-
-Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
-
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  
-
----
diff --git a/_includes/cwl/1st-tool.cwl b/_includes/cwl/1st-tool.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/1st-workflow.cwl b/_includes/cwl/1st-workflow.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: Workflow
 inputs:
diff --git a/_includes/cwl/arguments.cwl b/_includes/cwl/arguments.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 label: Example trivial wrapper for Java 7 compiler
diff --git a/_includes/cwl/array-inputs.cwl b/_includes/cwl/array-inputs.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
diff --git a/_includes/cwl/array-outputs.cwl b/_includes/cwl/array-outputs.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: touch
diff --git a/_includes/cwl/createfile.cwl b/_includes/cwl/createfile.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 class: CommandLineTool
 cwlVersion: v1.0
 baseCommand: ["cat", "example.conf"]
diff --git a/_includes/cwl/docker.cwl b/_includes/cwl/docker.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: node
diff --git a/_includes/cwl/env.cwl b/_includes/cwl/env.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: env
diff --git a/_includes/cwl/expression.cwl b/_includes/cwl/expression.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/inp.cwl b/_includes/cwl/inp.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/linkfile.cwl b/_includes/cwl/linkfile.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 hints:
diff --git a/_includes/cwl/nestedworkflows.cwl b/_includes/cwl/nestedworkflows.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: Workflow
 
diff --git a/_includes/cwl/record.cwl b/_includes/cwl/record.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
diff --git a/_includes/cwl/stdout.cwl b/_includes/cwl/stdout.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/tar-param.cwl b/_includes/cwl/tar-param.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: [tar, xf]
diff --git a/_includes/cwl/tar.cwl b/_includes/cwl/tar.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: [tar, xf]
diff --git a/setup.md b/setup.md
@@ -3,4 +3,20 @@ layout: page
 title: Setup
 permalink: /setup/
 ---
-FIXME
+To follow the Common Workflow Language user guide, you will need an up-to-date
+Linux or Mac OS X system, with the following software installed:
+
+- A text editor with YAML support
+- A CWL implementation to run the described tools and workflows. When first
+getting started with CWL, we recommend the reference implementation,
+[`cwltool`][ref-imp]. You can find a full list on
+[the project homepage][commonwl].
+- Most of the software tools used in the user guide are standard UNIX commands
+(`cat`, `echo`, `env`, `tar`, `touch`, `wc`), but to run all examples you will
+also need:
+  - node.js
+  - Java compiler
+  - Docker (optional)
+
+[ref-imp]: https://github.com/common-workflow-language/cwltool
+[commonwl]: http://www.commonwl.org/

-Original file line number
+Diff line change
@@ @@ -1,9 +0,0 @@ @@
 -Please delete the text below before submitting your contribution.
+-
 ----
+-
 -Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.
+-
 -Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).
+-
 ----
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+#!/usr/bin/env cwl-runner`
	`2`	`+`
`1`	`3`	`cwlVersion: v1.0`
`2`	`4`	`class: CommandLineTool`
`3`	`5`	`baseCommand: echo`