From f56e88606944c82a3a3a92d7626e30b81acdcfae Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Sun, 3 Sep 2017 15:51:26 -0700 Subject: [PATCH] Deal with bcftools config header --- debian/patches/bcftools-config-header.patch | 19 +++++++++++++++++++ debian/patches/series | 1 + debian/rules | 3 ++- 3 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 debian/patches/bcftools-config-header.patch create mode 100644 debian/patches/series diff --git a/debian/patches/bcftools-config-header.patch b/debian/patches/bcftools-config-header.patch new file mode 100644 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 +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 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 8f998dd..d062880 100755 --- 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.% -- 2.30.2