Deal with bcftools config header

diff --git a/debian/patches/bcftools-config-header.patch b/debian/patches/bcftools-config-header.patch
new file mode 100644 (file)
index 0000000..21bc1ad
--- /dev/null
+++ b/debian/patches/bcftools-config-header.patch
@@ -0,0 +1,19 @@
+Description: create bcftools/config.h if it doesn't exist
+ since bcftools and samtools 1.5 are using the same build system,
+ they need to be treated the same way. Compilation fails when bcftools
+ can't find its config.h.
+Author: Afif Elghraoui <afif@debian.org>
+Forwarded: https://github.com/pysam-developers/pysam/pull/533
+Last-Update: 2017-09-03
+--- python-pysam.orig/setup.py
++++ python-pysam/setup.py
+@@ -134,7 +134,8 @@
+ package_dirs = {'pysam': 'pysam',
+                 'pysam.include.samtools': 'samtools',
+                 'pysam.include.bcftools': 'bcftools'}
+-config_headers = ["samtools/config.h"]
++config_headers = ["samtools/config.h",
++                  "bcftools/config.h"]
+ 
+ from cy_build import CyExtension as Extension, cy_build_ext as build_ext
+ 

diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644 (file)
index 0000000..336b8e8
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+bcftools-config-header.patch

diff --git a/debian/rules b/debian/rules
index 8f998dd09de013f339c1c80f0ca5e03b9ea829ad..d062880b06914ef1446c000b91715e21d5c48a83 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -44,7 +44,8 @@ override_dh_auto_clean:
                pysam/config.py \
                pysam/config.h \
                pysam/lib*.c \
-               samtools/config.h
+               samtools/config.h \
+               bcftools/config.h
        rm -rf pysam.egg-info
 
 .PHONY: pysam_data.% cbcf_data.%