[med-svn] [sambamba] 01/01: Try to use debian packaged libs

Andreas Tille tille at debian.org
Sun Apr 16 12:36:33 UTC 2017


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tille pushed a commit to branch master
in repository sambamba.

commit 4a711d034088b3b258995ae0922a49c37396552e
Author: Andreas Tille <tille at debian.org>
Date:   Sun Apr 16 14:36:04 2017 +0200

    Try to use debian packaged libs
---
 debian/control                                |  3 ++-
 debian/patches/use_debian_packaged_libs.patch | 11 +++++++++--
 debian/rules                                  |  4 ++--
 3 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/debian/control b/debian/control
index fe55d95..f677eaa 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,8 @@ Build-Depends: debhelper (>= 10),
                libundead-dev,
                libbiod-dev,
                liblz4-dev,
-               libhts-dev
+               libhts-dev,
+               python
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sambamba.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/sambamba.git
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
index af6a043..d016ee3 100644
--- a/debian/patches/use_debian_packaged_libs.patch
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -4,8 +4,10 @@ Desciption: Use Debian packaged lz4 and htslib
 
 --- a/Makefile
 +++ b/Makefile
-@@ -2,8 +2,7 @@ D_COMPILER=dmd
- D_FLAGS=--compiler=dmd -IBioD -IundeaD/src -g -d#-O -release -inline # -version=serial
+@@ -1,9 +1,8 @@
+ D_COMPILER=dmd
+-D_FLAGS=--compiler=dmd -IBioD -IundeaD/src -g -d#-O -release -inline # -version=serial
++D_FLAGS=--compiler=dmd -g -d#-O -release -inline # -version=serial
  LDMD=ldmd2
  
 -STATIC_LIB_PATH=-Lhtslib -Llz4/lib
@@ -58,3 +60,8 @@ Desciption: Use Debian packaged lz4 and htslib
  
  clean-d:
  	rm -rf build/*
+--- a/sambamba-ldmd-release.rsp
++++ b/sambamba-ldmd-release.rsp
+@@ -1 +1 @@
+-"-g" "-O2" "-c" "-m64" "-release" "-IBioD/" "-IundeaD/src/" "-ofbuild/sambamba.o" "-odbuild" "-I." "main.d" "BioD/bio/bam/baifile.d" "sambamba/depth.d" "BioD/bio/core/utils/switchendianness.d" "sambamba/utils/common/readstorage.d" "BioD/bio/core/utils/tmpfile.d" "sambamba/utils/common/bed.d" "BioD/bio/bam/utils/samheadermerger.d" "thirdparty/mergesort.d" "BioD/bio/bam/readrange.d" "cram/exception.d" "sambamba/utils/view/headerserializer.d" "BioD/bio/bam/splitter.d" "cram/htslib.d" "BioD [...]
++"-g" "-O2" "-c" "-m64" "-release" "-ofbuild/sambamba.o" "-odbuild" "-I." "main.d" "sambamba/depth.d" "sambamba/utils/common/readstorage.d" "sambamba/utils/common/bed.d" "thirdparty/mergesort.d" "cram/exception.d" "sambamba/utils/view/headerserializer.d" "cram/htslib.d" "sambamba/utils/common/ldc_gc_workaround.d" "sambamba/utils/common/filtering.d" "sambamba/utils/common/queryparser.d" "cram/reader.d" "sambamba/utils/common/overwrite.d" "sambamba/index.d" "sambamba/markdup.d" "cram/refer [...]
diff --git a/debian/rules b/debian/rules
index ef8a267..58849b3 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,7 +10,7 @@ export LC_ALL=C.UTF-8
 	dh $@
 
 override_dh_auto_clean:
-	dh_auto_clean --buildsystem=makefile -- -f Makefile.guix
+	rm -rf build/
 
 override_dh_auto_build:
-	dh_auto_build --buildsystem=makefile -- -f Makefile.guix
+	make sambamba-ldmd2-64

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