This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository pbbam.
commit f9eebad32678915381ec242a736dc124d210b1fe Author: Afif Elghraoui <[email protected]> Date: Mon Jul 4 19:28:28 2016 -0700 Set up build-time tests for command-line tools --- debian/control | 4 +++- debian/patches/remove-bam2sam.patch | 18 ++++++++++++++++++ debian/patches/series | 1 + debian/rules | 16 ++++++++++++++-- 4 files changed, 36 insertions(+), 3 deletions(-) diff --git a/debian/control b/debian/control index cb0a7ef..32e4b7a 100644 --- a/debian/control +++ b/debian/control @@ -9,11 +9,13 @@ Build-Depends: cmake, # swig3.0, doxygen, -# libgtest-dev, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, +# Test-Depends: +# libgtest-dev, + python-cram, samtools, Standards-Version: 3.9.8 Homepage: https://github.com/PacificBiosciences/pbbam diff --git a/debian/patches/remove-bam2sam.patch b/debian/patches/remove-bam2sam.patch new file mode 100644 index 0000000..df2447d --- /dev/null +++ b/debian/patches/remove-bam2sam.patch @@ -0,0 +1,18 @@ +Description: Exclude the bam2sam utility + It is a convenience tool provided by upstream to avoid depending on + samtools. We actually have trouble building it in Debian and have + easy access to samtools. +Author: Afif Elghraoui <[email protected]> +Forwarded: not-needed +Last-Update: 2016-07-04 + +--- pbbam.orig/tools/CMakeLists.txt ++++ pbbam/tools/CMakeLists.txt +@@ -11,7 +11,6 @@ + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PacBioBAM_CXX_FLAGS}") + + # tools +-add_subdirectory(bam2sam) + add_subdirectory(pbindex) + add_subdirectory(pbindexdump) + add_subdirectory(pbmerge) diff --git a/debian/patches/series b/debian/patches/series index 59337a9..c87ab09 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ dont-try-building-gtest.patch ssl-md5.patch +remove-bam2sam.patch diff --git a/debian/rules b/debian/rules index cef8524..fcc0aa0 100755 --- a/debian/rules +++ b/debian/rules @@ -19,8 +19,8 @@ override_dh_auto_configure: # -DPacBioBAM_wrap_python=ON \ # -DPacBioBAM_wrap_r=ON -override_dh_auto_test: -# cd build && $(MAKE) test +override_dh_auto_test: $(subst .t,.deb.t,$(wildcard tests/src/cram/pb*.t)) + TESTDIR=tests/src/cram cram -v $^ override_dh_link: dh_link --package=libpbbam-dev \ @@ -30,3 +30,15 @@ override_dh_link: override_dh_installchangelogs: dh_installchangelogs CHANGELOG.md + +override_dh_auto_clean: + dh_auto_clean + find -name "*.deb.t" -delete + +%.deb.t: %.t + sed \ + -e 's/$$BAM2SAM/samtools view/g' \ + -e 's/\-\-header\-only/-H/g' \ + -e 's/\-\-no\-header//g' \ + $< > $@ + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbbam.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
