[med-svn] [ariba] 07/14: use Debian packaged libraries for extension building

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 571dd9b8ff74d2248a2d4d5ef36c1011d33b2432
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jul 31 18:13:27 2016 +0000

    use Debian packaged libraries for extension building
---
 debian/patches/series                              |  1 +
 .../use_debian_packaged_libs_for_extension.patch   | 82 ++++++++++++++++++++++
 2 files changed, 83 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 11fb5eb..2fdf295 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 rename-cdhit.patch
+use_debian_packaged_libs_for_extension.patch
diff --git a/debian/patches/use_debian_packaged_libs_for_extension.patch b/debian/patches/use_debian_packaged_libs_for_extension.patch
new file mode 100644
index 0000000..a12cf4c
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libs_for_extension.patch
@@ -0,0 +1,82 @@
+--- a/setup.py
++++ b/setup.py
+@@ -4,47 +4,46 @@
+ import glob
+ from setuptools import setup, find_packages, Extension
+ 
+-minimap_c_files = [
+-    'bseq.c',
+-    'index.c',
+-    'kthread.c',
+-    'map.c',
+-    'misc.c',
+-    'sdust.c',
+-    'sketch.c',
+-]
+-
+-minimap_c_files = [os.path.join('third_party', 'minimap-0.2', x) for x in minimap_c_files]
+-minimap_c_files.append(os.path.join('ariba', 'ext', 'minimap_ariba.cpp'))
++#minimap_c_files = [
++#    'bseq.c',
++#    'index.c',
++#    'kthread.c',
++#    'map.c',
++#    'misc.c',
++#    'sdust.c',
++#    'sketch.c',
++#]
++#minimap_c_files = [os.path.join('third_party', 'minimap-0.2', x) for x in minimap_c_files]
++minimap_c_files = [os.path.join('ariba', 'ext', 'minimap_ariba.cpp')]
+ minimap_mod = Extension(
+     "minimap_ariba",
+     minimap_c_files,
+-    extra_link_args=['-lz'],
+-    include_dirs=[os.path.join('third_party', 'minimap-0.2')],
++    extra_link_args=['-lz', '-lminimap'],
++    include_dirs=[os.path.join(os.path.sep, 'usr', 'include', 'minimap')],
+ )
+ 
+-fermilite_c_files = [
+-    'bfc.c',
+-    'bseq.c',
+-    'bubble.c',
+-    'htab.c',
+-    'ksw.c',
+-    'kthread.c',
+-    'mag.c',
+-    'misc.c',
+-    'mrope.c',
+-    'rld0.c',
+-    'rle.c',
+-    'rope.c',
+-    'unitig.c'
+-]
+-fermilite_c_files = [os.path.join('third_party', 'fermi-lite-0.1', x) for x in fermilite_c_files]
+-fermilite_c_files.append(os.path.join('ariba', 'ext', 'fml-asm_ariba.cpp'))
++#fermilite_c_files = [
++#    'bfc.c',
++#    'bseq.c',
++#    'bubble.c',
++#    'htab.c',
++#    'ksw.c',
++#    'kthread.c',
++#    'mag.c',
++#    'misc.c',
++#    'mrope.c',
++#    'rld0.c',
++#    'rle.c',
++#    'rope.c',
++#    'unitig.c'
++#]
++#fermilite_c_files = [os.path.join('third_party', 'fermi-lite-0.1', x) for x in fermilite_c_files]
++fermilite_c_files = [os.path.join('ariba', 'ext', 'fml-asm_ariba.cpp')]
+ fermilite_mod = Extension(
+     "fermilite_ariba",
+     fermilite_c_files,
+-    extra_link_args=['-lz'],
+-    include_dirs=[os.path.join('third_party', 'fermi-lite-0.1')],
++    extra_link_args=['-lz', '-lfml'],
++    #include_dirs=[os.path.join('third_party', 'fermi-lite-0.1')],
+ )
+ 
+ 

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