[med-svn] [spades] 03/05: use fully qualified config paths

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository spades.

commit 300d4a80135ec041c63c6fdbce4105e9132f496a
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sat Feb 6 19:45:56 2016 +0000

    use fully qualified config paths
---
 debian/patches/0111_use_full_config_dirs.patch | 21 +++++++++++++++++++++
 debian/patches/series                          |  1 +
 2 files changed, 22 insertions(+)

diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch
new file mode 100644
index 0000000..8979c6d
--- /dev/null
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -0,0 +1,21 @@
+--- a/src/spades_pipeline/spades_logic.py
++++ b/src/spades_pipeline/spades_logic.py
+@@ -134,8 +134,18 @@
+         dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
+         # removing template configs
+         for root, dirs, files in os.walk(dst_configs):
++            replacements = {'#include "': ('#include "' + root + '/')}
+             for cfg_file in files:
+                 cfg_file = os.path.join(root, cfg_file)
++                lines = []
++                with open(cfg_file) as infile:
++                    for line in infile:
++                        for src, target in replacements.iteritems():
++                            line = line.replace(src, target)
++                        lines.append(line)
++                with open(cfg_file, 'w') as outfile:
++                    for line in lines:
++                        outfile.write(line)
+                 if cfg_file.endswith('.info.template'):
+                     if os.path.isfile(cfg_file.split('.template')[0]):
+                         os.remove(cfg_file)
diff --git a/debian/patches/series b/debian/patches/series
index ce92b7a..b32ddb5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -11,3 +11,4 @@
 # use-debian-packaged-bamtools.patch   ## <<-- does not work - see patch description
 # use-debian-packaged-yaml-cpp.patch   ## <<-- does not work - see patch description
 0110_build_single_thread.patch
+0111_use_full_config_dirs.patch

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