Do not use internal htslib

Test suite passes. The patch needs to be generalized before forwarding
upstream.

diff --git a/debian/patches/htslib-external-config.patch b/debian/patches/htslib-external-config.patch
new file mode 100644 (file)
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@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 da8b79080b4d9bdb52ef264ac43f936283f0956a..af88631bc1c353ed3a4d1b207a2dd00e11f4cb61 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 rpath.patch
+htslib-external-config.patch