[med-svn] [spades] 03/06: refresh patches

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository spades.

commit 1cb97c4c8028291b370c0d6874ab37a1250e247c
Author: Sascha Steinbiss <satta at debian.org>
Date:   Mon Jul 11 08:39:44 2016 +0000

    refresh patches
---
 debian/patches/0111_use_full_config_dirs.patch |  2 +-
 debian/patches/0113_adjust_paths.patch         | 17 ++++++++++++-----
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch
index 0de6fe9..0807c62 100644
--- a/debian/patches/0111_use_full_config_dirs.patch
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <satta at debian.org>
      #print("Calling: " + " ".join(command))
      support.sys_call(command, log)
  
-@@ -225,6 +239,19 @@
+@@ -226,6 +240,19 @@
      command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
      add_configs(command, dst_configs)
      log.info(str(command))
diff --git a/debian/patches/0113_adjust_paths.patch b/debian/patches/0113_adjust_paths.patch
index 52f6055..35e4b8a 100644
--- a/debian/patches/0113_adjust_paths.patch
+++ b/debian/patches/0113_adjust_paths.patch
@@ -4,20 +4,27 @@ Description: adjust runtime paths
 Author: Sascha Steinbiss <satta at debian.org>
 --- a/spades_init.py
 +++ b/spades_init.py
-@@ -25,7 +25,12 @@
+@@ -29,7 +29,12 @@
      global ext_python_modules_home
  
      # users configuration (spades_init.py and spades binary are in the same directory)
--    if os.path.isfile(os.path.join(spades_home, 'spades')):
+-    if isfile(os.path.join(spades_home, 'spades')):
 +    if os.path.isfile('/usr/lib/spades/bin/spades'):
 +        bin_home = '/usr/lib/spades/bin/'
 +        spades_home = '/usr/share/spades'
 +        python_modules_home = spades_home
 +        ext_python_modules_home = spades_home
 +    elif os.path.isfile(os.path.join(spades_home, 'spades')):
-         install_prefix = os.path.dirname(spades_home)
-         bin_home = os.path.join(install_prefix, 'bin')
-         spades_home = os.path.join(install_prefix, 'share', 'spades')
+         install_prefix = dirname(spades_home)
+         bin_home = join(install_prefix, 'bin')
+         spades_home = join(install_prefix, 'share', 'spades')
+@@ -44,4 +49,4 @@
+ 
+ if __name__ == '__main__':
+     spades_py_path = join(dirname(realpath(__file__)), 'spades.py')
+-    sys.stderr.write('Please use ' + spades_py_path + ' for running SPAdes genome assembler\n')
+\ No newline at end of file
++    sys.stderr.write('Please use ' + spades_py_path + ' for running SPAdes genome assembler\n')
 --- a/truspades.py
 +++ b/truspades.py
 @@ -13,8 +13,14 @@

-- 
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