[med-svn] [python-pysam] 01/01: Do not use internal htslib

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-pysam.

commit a849526ef557f20f9c50f6c2f3da24acfe32900a
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Jan 26 04:12:46 2017 -0800

    Do not use internal htslib
    
    Test suite passes. The patch needs to be generalized before forwarding
    upstream.
---
 debian/patches/htslib-external-config.patch | 15 +++++++++++++++
 debian/patches/series                       |  1 +
 2 files changed, 16 insertions(+)

diff --git a/debian/patches/htslib-external-config.patch b/debian/patches/htslib-external-config.patch
new file mode 100644
index 0000000..ab7a144
--- /dev/null
+++ b/debian/patches/htslib-external-config.patch
@@ -0,0 +1,15 @@
+Description: Do not use internal htslib library
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2017-01-26
+--- python-pysam.orig/setup.py
++++ python-pysam/setup.py
+@@ -255,7 +255,7 @@
+ else:
+     raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
+ 
+-internal_htslib_libraries = [os.path.splitext("chtslib{}".format(sysconfig.get_config_var('SO')))[0]]
++internal_htslib_libraries = []
+ 
+ # build config.py
+ with open(os.path.join("pysam", "config.py"), "w") as outf:
diff --git a/debian/patches/series b/debian/patches/series
index da8b790..af88631 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 rpath.patch
+htslib-external-config.patch

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