This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository spades.
commit 6831be967c5eb4511e86b52d3bf8e71014ea010a Author: Sascha Steinbiss <[email protected]> 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 <[email protected]> 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 <[email protected]> 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') -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
