[med-svn] [spades] 04/08: patch spades_init.py to look in correct paths

[Sascha Steinbiss]

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

commit 297fbe0743da79d593758a95cb5d9f187dec0956
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Feb 11 11:30:07 2016 +0000

    patch spades_init.py to look in correct paths
---
 debian/patches/0113_add_hashbang.patch |  9 ---------
 debian/patches/0113_adjust_paths.patch | 20 ++++++++++++++++++++
 debian/patches/series                  |  2 +-
 3 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/debian/patches/0113_add_hashbang.patch b/debian/patches/0113_add_hashbang.patch
deleted file mode 100644
index 573a385..0000000
--- a/debian/patches/0113_add_hashbang.patch
+++ /dev/null
@@ -1,9 +0,0 @@
-Description: add hashbang line to script
-Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/spades_init.py
-+++ b/spades_init.py
-@@ -1,3 +1,4 @@
-+#!/usr/bin/env python
- ############################################################################
- # Copyright (c) 2015 Saint Petersburg State University
- # Copyright (c) 2011-2014 Saint Petersburg Academic University
diff --git a/debian/patches/0113_adjust_paths.patch b/debian/patches/0113_adjust_paths.patch
new file mode 100644
index 0000000..7532e56
--- /dev/null
+++ b/debian/patches/0113_adjust_paths.patch
@@ -0,0 +1,20 @@
+Description: adjust runtime paths 
+ Debian stores components od SPAdes in different places than expected by
+ upstream. This patch makes it look in the right locations.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/spades_init.py
++++ b/spades_init.py
+@@ -25,7 +25,12 @@
+     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 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')
diff --git a/debian/patches/series b/debian/patches/series
index 48cf49d..3d8c8f0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -13,4 +13,4 @@
 0110_build_single_thread.patch
 0111_use_full_config_dirs.patch
 0112_spelling.patch
-0113_add_hashbang.patch
+0113_adjust_paths.patch

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