[med-svn] [mapdamage] 03/05: Make sure seqtk will be found

[Andreas Tille]

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tille pushed a commit to branch master
in repository mapdamage.

commit a14466a2895b8bbac81e5af199973f1e69896451
Author: Andreas Tille <tille at debian.org>
Date:   Tue Aug 2 09:41:13 2016 +0200

    Make sure seqtk will be found
---
 debian/control                                 |  3 ++-
 debian/patches/use_debian_packaged_seqtk.patch | 11 +++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index c883ea9..bfba1b4 100644
--- a/debian/control
+++ b/debian/control
@@ -15,7 +15,8 @@ Homepage: https://ginolhac.github.io/mapDamage/
 Package: mapdamage
 Architecture: all
 Depends: ${python:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         r-base-core
 Description: tracking and quantifying damage patterns in ancient DNA sequences
  MapDamage is a computational framework written in Python and R, which
  tracks and quantifies DNA damage patterns among ancient DNA sequencing
diff --git a/debian/patches/use_debian_packaged_seqtk.patch b/debian/patches/use_debian_packaged_seqtk.patch
index c845341..97cffca 100644
--- a/debian/patches/use_debian_packaged_seqtk.patch
+++ b/debian/patches/use_debian_packaged_seqtk.patch
@@ -52,3 +52,14 @@ Description: Use Debian packaged seqtk
      scripts=['bin/mapDamage'],
      url='https://github.com/ginolhac/mapDamage',
      license='LICENSE.txt',
+--- a/bin/mapDamage
++++ b/bin/mapDamage
+@@ -151,7 +151,7 @@ def main():
+         sys.path.insert(0,path_to_mm)
+     import mapdamage
+ 
+-    fpath_seqtk = mapdamage.rscript.construct_path("seqtk", folder="seqtk")
++    fpath_seqtk = '/usr/bin/seqtk'
+     if not (os.path.isfile(fpath_seqtk) and os.access(fpath_seqtk, os.X_OK)):
+         sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n"
+                          "been intalled properly or current user does not\n"

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