[med-svn] [mapdamage] 01/02: edit path to debian packaged seqtk

[Nadiya Sitdykova]

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rovenskasa-guest pushed a commit to branch master
in repository mapdamage.

commit 2c8a666ff5435814055790a1ca5592a9d396f7d9
Author: nadiya <nadiya at debian>
Date:   Sat Mar 25 22:27:01 2017 -0400

    edit path to debian packaged seqtk
---
 debian/changelog                               |  8 +++++++
 debian/patches/use_debian_packaged_seqtk.patch | 33 +++++++++++++++++++-------
 2 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 0992c7d..f1818f9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+mapdamage (2.0.6+dfsg-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * 
+
+ -- nadiya <nadiya at debian>  Sat, 25 Mar 2017 22:20:38 -0400
+
 mapdamage (2.0.6+dfsg-2) UNRELEASED; urgency=medium
 
   * Team upload
@@ -16,6 +23,7 @@ mapdamage (2.0.6+dfsg-2) UNRELEASED; urgency=medium
   * Add test checking stdin redirect
   * Add simple test to demonstrate the problems with installing
     r-cran-rcppgsl package
+  * Edit path to seqtk in composition.py
 
  -- rovenskasa-guest <rovenskasa at gmail.com>  Thu, 23 Mar 2017 21:34:41 -0700
 
diff --git a/debian/patches/use_debian_packaged_seqtk.patch b/debian/patches/use_debian_packaged_seqtk.patch
index 97cffca..ce7658d 100644
--- a/debian/patches/use_debian_packaged_seqtk.patch
+++ b/debian/patches/use_debian_packaged_seqtk.patch
@@ -2,9 +2,11 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Thu, 28 Jul 2016 15:13:14 +0200
 Description: Use Debian packaged seqtk
 
---- a/setup.py
-+++ b/setup.py
-@@ -6,21 +6,6 @@ from distutils.command.install import in
+Index: mapdamage/setup.py
+===================================================================
+--- mapdamage.orig/setup.py	2017-03-25 21:05:13.530450881 -0400
++++ mapdamage/setup.py	2017-03-25 21:48:04.000000000 -0400
+@@ -6,21 +6,6 @@
  import os
  import subprocess
  
@@ -26,7 +28,7 @@ Description: Use Debian packaged seqtk
  def setup_version():
      if not os.path.exists(".git"):
          # Release version, no .git folder
-@@ -40,16 +25,7 @@ class compileInstall(DistutilsInstall):
+@@ -40,16 +25,7 @@
      def run(self):
          self.record=""
          setup_version()
@@ -43,7 +45,7 @@ Description: Use Debian packaged seqtk
  
  
  setup(
-@@ -59,7 +35,7 @@ setup(
+@@ -59,7 +35,7 @@
      author='Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson',
      author_email='MSchubert at snm.ku.dk, jonsson.hakon at gmail.com',
      packages=['mapdamage'],
@@ -52,9 +54,11 @@ 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():
+Index: mapdamage/bin/mapDamage
+===================================================================
+--- mapdamage.orig/bin/mapDamage	2017-03-25 21:05:13.518450694 -0400
++++ mapdamage/bin/mapDamage	2017-03-25 21:48:04.000000000 -0400
+@@ -151,7 +151,7 @@
          sys.path.insert(0,path_to_mm)
      import mapdamage
  
@@ -63,3 +67,16 @@ Description: Use Debian packaged 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"
+Index: mapdamage/mapdamage/composition.py
+===================================================================
+--- mapdamage.orig/mapdamage/composition.py	2017-03-25 21:05:13.530450881 -0400
++++ mapdamage/mapdamage/composition.py	2017-03-25 22:10:29.760815637 -0400
+@@ -35,7 +35,7 @@
+     Gets the basecomposition of all the sequences in filename
+     and returns the value to destination if given.
+     """
+-    path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk") 
++    path_to_seqtk = "/usr/bin/seqtk" 
+     bases = {"A":0,"C":0,"G":0,"T":0}
+     alp = ["A","C","G","T"]
+     try:

-- 
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