This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository spades.
commit 1cb97c4c8028291b370c0d6874ab37a1250e247c Author: Sascha Steinbiss <[email protected]> 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 <[email protected]> #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 <[email protected]> --- 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 @@ -- 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
