[med-svn] [spades] 07/08: extend patches

[Sascha Steinbiss]

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

commit 6831be967c5eb4511e86b52d3bf8e71014ea010a
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Feb 11 15:12:19 2016 +0000

    extend patches
---
 debian/patches/0111_use_full_config_dirs.patch | 61 ++++++++++++++++++++++++++
 debian/patches/0113_adjust_paths.patch         | 15 +++++++
 2 files changed, 76 insertions(+)

diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch
index 5c3c78b..fa4ec01 100644
--- a/debian/patches/0111_use_full_config_dirs.patch
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -23,3 +23,64 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
                  if cfg_file.endswith('.info.template'):
                      if os.path.isfile(cfg_file.split('.template')[0]):
                          os.remove(cfg_file)
+@@ -194,6 +204,18 @@
+     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)
+         for cfg_file in files:
+             cfg_file = os.path.join(root, cfg_file)
+             if cfg_file.endswith('.info.template'):
+--- a/src/spades_pipeline/corrector_logic.py
++++ b/src/spades_pipeline/corrector_logic.py
+@@ -51,6 +51,18 @@
+     cfg_file_name = os.path.join(dst_configs, "corrector.info")
+     # 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)
+         for cfg_file in files:
+             cfg_file = os.path.join(root, cfg_file)
+             if cfg_file.endswith('.template'):
+--- a/src/spades_pipeline/hammer_logic.py
++++ b/src/spades_pipeline/hammer_logic.py
+@@ -109,6 +109,18 @@
+         cfg_file_name = os.path.join(dst_configs, "config.info")
+     # 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)
+         for cfg_file in files:
+             cfg_file = os.path.join(root, cfg_file)
+             if cfg_file.endswith('.template'):
diff --git a/debian/patches/0113_adjust_paths.patch b/debian/patches/0113_adjust_paths.patch
index 7532e56..4118064 100644
--- a/debian/patches/0113_adjust_paths.patch
+++ b/debian/patches/0113_adjust_paths.patch
@@ -18,3 +18,18 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
          install_prefix = os.path.dirname(spades_home)
          bin_home = os.path.join(install_prefix, 'bin')
          spades_home = os.path.join(install_prefix, 'share', 'spades')
+--- a/truspades.py
++++ b/truspades.py
+@@ -14,7 +14,11 @@
+ bin_home = os.path.join(truspades_home, 'bin')
+ python_modules_home = os.path.join(truspades_home, 'src')
+ 
+-if os.path.isfile(os.path.join(truspades_home, 'spades')):
++if os.path.isfile('/usr/lib/spades/bin/spades'):
++    bin_home = '/usr/lib/spades/bin/'
++    truspades_home = '/usr/share/spades'
++    python_modules_home = truspades_home
++elif os.path.isfile(os.path.join(truspades_home, 'spades')):
+     install_prefix = os.path.dirname(truspades_home)
+     bin_home = os.path.join(install_prefix, 'bin')
+     truspades_home = os.path.join(install_prefix, 'share', 'spades')

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