[med-svn] samtools 06/07: Add recommends to cwl-tool and fix shebang line of cwl scripts

[Andreas Tille]

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tille pushed a commit to branch debian/unstable
in repository samtools.

commit d3b6113420da7dad521d9ce5f53c9a9148b95148
Author: Andreas Tille <tille at debian.org>
Date:   Fri Aug 4 17:56:47 2017 +0200

    Add recommends to cwl-tool and fix shebang line of cwl scripts
---
 debian/changelog          | 1 +
 debian/control            | 3 ++-
 debian/samtools-faidx.cwl | 2 +-
 debian/samtools-index.cwl | 2 +-
 debian/samtools-rmdup.cwl | 2 +-
 debian/samtools-sort.cwl  | 2 +-
 debian/samtools-view.cwl  | 2 +-
 7 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 3468862..ef4696f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ samtools (1.5-1) UNRELEASED; urgency=medium
   * debhelper 10
   * Standards-Version: 4.0.0 (no changes needed)
   * Bump versioned Build-Depends: libhts-dev (>= 1.5)
+  * Add recommends to cwl-tool and fix shebang line of cwl scripts
 
  -- Andreas Tille <tille at debian.org>  Thu, 20 Jul 2017 12:14:48 +0200
 
diff --git a/debian/control b/debian/control
index ffd7090..cc4a03a 100644
--- a/debian/control
+++ b/debian/control
@@ -25,7 +25,8 @@ Package: samtools
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
-Recommends: python
+Recommends: python,
+            cwltool
 Description: processing sequence alignments in SAM and BAM formats
  Samtools is a set of utilities that manipulate nucleotide sequence alignments
  in the binary BAM format. It imports from and exports to the ascii SAM
diff --git a/debian/samtools-faidx.cwl b/debian/samtools-faidx.cwl
index 203c1c0..0eb7011 100755
--- a/debian/samtools-faidx.cwl
+++ b/debian/samtools-faidx.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwl-runner
+#!/usr/bin/cwl-runner
 #
 # To use it as stand alone tool. The working directory should not have input .fa file
 #    example: "./samtools-faidx.cwl --input=./test-files/mm10.fa"
diff --git a/debian/samtools-index.cwl b/debian/samtools-index.cwl
index 9bdc5b1..69b4c2c 100755
--- a/debian/samtools-index.cwl
+++ b/debian/samtools-index.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwl-runner
+#!/usr/bin/cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/debian/samtools-rmdup.cwl b/debian/samtools-rmdup.cwl
index 196a8e9..85092a8 100755
--- a/debian/samtools-rmdup.cwl
+++ b/debian/samtools-rmdup.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwl-runner
+#!/usr/bin/cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/debian/samtools-sort.cwl b/debian/samtools-sort.cwl
index 77b5a85..4adefa0 100755
--- a/debian/samtools-sort.cwl
+++ b/debian/samtools-sort.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwl-runner
+#!/usr/bin/cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/debian/samtools-view.cwl b/debian/samtools-view.cwl
index f1b1d94..c204d98 100755
--- a/debian/samtools-view.cwl
+++ b/debian/samtools-view.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwl-runner
+#!/usr/bin/cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool

-- 
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