Update packaging for external htslib link due to build system changes

diff --git a/debian/patches/adding-include-hts-dirs b/debian/patches/adding-include-hts-dirs
deleted file mode 100644 (file)
index 5f3194c..0000000
--- a/debian/patches/adding-include-hts-dirs
+++ /dev/null
@@ -1,11 +0,0 @@
-Description: Added the include dirs
---- python-pysam.orig/setup.py
-+++ python-pysam/setup.py
-@@ -116,6 +116,7 @@
-     chtslib_sources = []
-     shared_htslib_sources = htslib_sources
-     htslib_library_dirs = HTSLIB_LIBRARY_DIR
-+    htslib_include_dirs = [HTSLIB_INCLUDE_DIR]
-     htslib_libraries = ['hts']
- else:
-     raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)

diff --git a/debian/patches/change-htslib-statement-to-link-to-debian b/debian/patches/change-htslib-statement-to-link-to-debian
deleted file mode 100644 (file)
index d607a0f..0000000
--- a/debian/patches/change-htslib-statement-to-link-to-debian
+++ /dev/null
@@ -1,25 +0,0 @@
-Description: Trying to bind to debian htslib
---- python-pysam.orig/setup.py
-+++ python-pysam/setup.py
-@@ -43,7 +43,7 @@
- #         pysam.
- # external: use shared libhts.so compiled outside of
- #           pysam
--HTSLIB_MODE = "separate"
-+HTSLIB_MODE = "external"
- HTSLIB_LIBRARY_DIR = os.environ.get('HTSLIB_LIBRARY_DIR', None)
- HTSLIB_INCLUDE_DIR = os.environ.get('HTSLIB_INCLUDE_DIR', None)
- 
-@@ -111,6 +111,12 @@
-     htslib_library_dirs = ['pysam']
-     htslib_include_dirs = ['htslib']
-     htslib_libraries = ['chtslib']
-+elif HTSLIB_MODE == 'external':
-+    htslib_sources = []
-+    chtslib_sources = []
-+    shared_htslib_sources = htslib_sources
-+    htslib_library_dirs = HTSLIB_LIBRARY_DIR
-+    htslib_libraries = ['hts']
- else:
-     raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
- 

diff --git a/debian/patches/series b/debian/patches/series
index d7785a372fc14e394be229c679fa1f0c3285cc30..878b5845b1f51e4692dde4694727a8aca5e8fbbe 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
-change-htslib-statement-to-link-to-debian
-adding-include-hts-dirs
 ignore-htslib-dir.patch
 disable-tests-requiring-network.patch

diff --git a/debian/rules b/debian/rules
index 126c2b5018ba62a414f33a5acea00fa6a6bdb519..cdf23f61e90988600cef2386a6f4c219687463ae 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -6,6 +6,7 @@ export PYBUILD_NAME=pysam
 
 TESTPKG    := $(DEB_SOURCE)-tests
 
+export HTSLIB_MODE=external
 HTSLIBDIR  := /usr/lib/$(DEB_HOST_MULTIARCH)
 export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
 export HTSLIB_INCLUDE_DIR=/usr/include