From 21aac6cb038456176c781b6ed74372c3820fd26f Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Wed, 11 Nov 2015 23:21:05 -0800 Subject: [PATCH] Refresh existing patches --- debian/patches/adding-include-hts-dirs | 2 +- debian/patches/change-htslib-statement-to-link-to-debian | 4 ++-- debian/patches/ignore-htslib-dir.patch | 6 +++--- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/debian/patches/adding-include-hts-dirs b/debian/patches/adding-include-hts-dirs index 129fa82..5f3194c 100644 --- a/debian/patches/adding-include-hts-dirs +++ b/debian/patches/adding-include-hts-dirs @@ -1,7 +1,7 @@ Description: Added the include dirs --- python-pysam.orig/setup.py +++ python-pysam/setup.py -@@ -103,6 +103,7 @@ +@@ -116,6 +116,7 @@ chtslib_sources = [] shared_htslib_sources = htslib_sources htslib_library_dirs = HTSLIB_LIBRARY_DIR diff --git a/debian/patches/change-htslib-statement-to-link-to-debian b/debian/patches/change-htslib-statement-to-link-to-debian index 045e302..d607a0f 100644 --- a/debian/patches/change-htslib-statement-to-link-to-debian +++ b/debian/patches/change-htslib-statement-to-link-to-debian @@ -1,7 +1,7 @@ Description: Trying to bind to debian htslib --- python-pysam.orig/setup.py +++ python-pysam/setup.py -@@ -30,7 +30,7 @@ +@@ -43,7 +43,7 @@ # pysam. # external: use shared libhts.so compiled outside of # pysam @@ -10,7 +10,7 @@ Description: Trying to bind to debian htslib HTSLIB_LIBRARY_DIR = os.environ.get('HTSLIB_LIBRARY_DIR', None) HTSLIB_INCLUDE_DIR = os.environ.get('HTSLIB_INCLUDE_DIR', None) -@@ -98,6 +98,12 @@ +@@ -111,6 +111,12 @@ htslib_library_dirs = ['pysam'] htslib_include_dirs = ['htslib'] htslib_libraries = ['chtslib'] diff --git a/debian/patches/ignore-htslib-dir.patch b/debian/patches/ignore-htslib-dir.patch index 0a73343..2ca4cd7 100644 --- a/debian/patches/ignore-htslib-dir.patch +++ b/debian/patches/ignore-htslib-dir.patch @@ -8,7 +8,7 @@ Last-Update: 2015-06-24 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- python-pysam.orig/setup.py +++ python-pysam/setup.py -@@ -476,8 +476,6 @@ +@@ -490,8 +490,6 @@ 'url': "https://github.com/pysam-developers/pysam", 'packages': ['pysam', 'pysam.include', @@ -17,8 +17,8 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ 'pysam.include.samtools', # 'pysam.include.samtools.bcftools', 'pysam.include.samtools.win32'], -@@ -493,7 +493,6 @@ - faidx], +@@ -509,7 +507,6 @@ + cutils], 'cmdclass': cmdclass, 'package_dir': {'pysam': 'pysam', - 'pysam.include.htslib': 'htslib', -- 2.30.2