specifying python2 as baseCommand in order for tests to work with systems where python3 is the default

Luka Stojanovic · Luka Stojanovic · commit 25975b0dc2d8 · 2016-12-08T19:48:52.000+01:00
diff --git a/v1.0/v1.0/bwa-mem-tool.cwl b/v1.0/v1.0/bwa-mem-tool.cwl
@@ -8,7 +8,7 @@ hints:
   - class: ResourceRequirement
     coresMin: 4
   - class: DockerRequirement
-    dockerPull: python
+    dockerPull: python:2-alpine
 
 inputs:
   - id: reference
diff --git a/v1.0/v1.0/index.py b/v1.0/v1.0/index.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
 
 # Toy program to generate inverted index of word to line.
 # Takes input text file on stdin and prints output index on stdout.
diff --git a/v1.0/v1.0/search.cwl b/v1.0/v1.0/search.cwl
@@ -2,7 +2,7 @@ cwlVersion: v1.0
 $graph:
 - id: index
   class: CommandLineTool
-  baseCommand: python
+  baseCommand: python2
   arguments:
     - valueFrom: input.txt
       position: 1
@@ -36,7 +36,7 @@ $graph:
 
 - id: search
   class: CommandLineTool
-  baseCommand: python
+  baseCommand: python2
   requirements:
     - class: InlineJavascriptRequirement
   inputs:
@@ -93,4 +93,4 @@ $graph:
       in:
         file: "#main/index/result"
         term: "#main/term"
-      out: [result]
+      out: [result]
diff --git a/v1.0/v1.0/search.py b/v1.0/v1.0/search.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
 
 # Toy program to search inverted index and print out each line the term
 # appears.
diff --git a/v1.0/v1.0/stagefile.cwl b/v1.0/v1.0/stagefile.cwl
@@ -13,7 +13,7 @@ outputs:
     type: File
     outputBinding:
       glob: bob.txt
-baseCommand: "python"
+baseCommand: "python2"
 arguments:
   - "-c"
   - |
diff --git a/v1.1.0-dev1/v1.1.0-dev1/bwa-mem-tool.cwl b/v1.1.0-dev1/v1.1.0-dev1/bwa-mem-tool.cwl
@@ -8,7 +8,7 @@ hints:
   - class: ResourceRequirement
     coresMin: 4
   - class: DockerRequirement
-    dockerPull: python
+    dockerPull: python:2-alpine
 
 inputs:
   - id: reference
diff --git a/v1.1.0-dev1/v1.1.0-dev1/index.py b/v1.1.0-dev1/v1.1.0-dev1/index.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
 
 # Toy program to generate inverted index of word to line.
 # Takes input text file on stdin and prints output index on stdout.
diff --git a/v1.1.0-dev1/v1.1.0-dev1/search.cwl b/v1.1.0-dev1/v1.1.0-dev1/search.cwl
@@ -2,7 +2,7 @@ cwlVersion: v1.1.0-dev1
 $graph:
 - id: index
   class: CommandLineTool
-  baseCommand: python
+  baseCommand: python2
   arguments:
     - valueFrom: input.txt
       position: 1
@@ -36,7 +36,7 @@ $graph:
 
 - id: search
   class: CommandLineTool
-  baseCommand: python
+  baseCommand: python2
   requirements:
     - class: InlineJavascriptRequirement
   inputs:
@@ -93,4 +93,4 @@ $graph:
       in:
         file: "#main/index/result"
         term: "#main/term"
-      out: [result]
+      out: [result]
diff --git a/v1.1.0-dev1/v1.1.0-dev1/search.py b/v1.1.0-dev1/v1.1.0-dev1/search.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
 
 # Toy program to search inverted index and print out each line the term
 # appears.
diff --git a/v1.1.0-dev1/v1.1.0-dev1/stagefile.cwl b/v1.1.0-dev1/v1.1.0-dev1/stagefile.cwl
@@ -13,7 +13,7 @@ outputs:
     type: File
     outputBinding:
       glob: bob.txt
-baseCommand: "python"
+baseCommand: "python2"
 arguments:
   - "-c"
   - |

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-#!/usr/bin/env python`
	`1`	`+#!/usr/bin/env python2`
`2`	`2`
`3`	`3`	`# Toy program to generate inverted index of word to line.`
`4`	`4`	`# Takes input text file on stdin and prints output index on stdout.`