specifying python2 as baseCommand in order for tests to work with sys…

…tems where python3 is the default
manu-chroma · Jan 16, 2017 · a4822d8 · a4822d8
1 parent 360e2b9
commit a4822d8
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Showing 10 changed files with 14 additions and 14 deletions.
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"
   - |