[med-svn] [pbbam] 01/01: Update patches
Afif Elghraoui
afif at moszumanska.debian.org
Sun Jan 22 00:28:52 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository pbbam.
commit 2e7d209029e0e3602fe191b05a93b0b5cdddbc0d
Author: Afif Elghraoui <afif at debian.org>
Date: Sun Dec 18 22:00:44 2016 -0800
Update patches
---
debian/patches/dont-try-building-gtest.patch | 26 -----
debian/patches/remove-bam2sam.patch | 14 +--
debian/patches/series | 2 -
debian/patches/use-PATH-for-test-programs.patch | 125 ------------------------
4 files changed, 7 insertions(+), 160 deletions(-)
diff --git a/debian/patches/dont-try-building-gtest.patch b/debian/patches/dont-try-building-gtest.patch
deleted file mode 100644
index d264b33..0000000
--- a/debian/patches/dont-try-building-gtest.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Description: Do not look for gtest sources
- The upstream build system expects to build gtest and specifies a location
- for its sources. Since we're using the Debian package, this variable is
- useless and gets in the way, so just get rid of it here.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-09-07
---- pbbam.orig/CMakeLists.txt
-+++ pbbam/CMakeLists.txt
-@@ -174,16 +174,6 @@
-
- if(PacBioBAM_build_tests)
-
-- if (NOT GTEST_SRC_DIR)
-- set(PREBUILT_GTEST_SRC ${PacBioBAM_RootDir}/../../../../prebuilt.tmpout/gtest/gtest_1.7.0/)
-- if(EXISTS ${PREBUILT_GTEST_SRC})
-- set(GTEST_SRC_DIR ${PREBUILT_GTEST_SRC})
-- else()
-- set(GTEST_SRC_DIR ../gtest) # keep old fallback behavior for external builds, for now at least
-- endif()
-- endif()
--
-- add_subdirectory(${GTEST_SRC_DIR} external/gtest/build)
- add_subdirectory(tests)
-
- endif()
diff --git a/debian/patches/remove-bam2sam.patch b/debian/patches/remove-bam2sam.patch
index df2447d..a4dec35 100644
--- a/debian/patches/remove-bam2sam.patch
+++ b/debian/patches/remove-bam2sam.patch
@@ -8,11 +8,11 @@ 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} ${PacBioBAM_CXX_FLAGS}")
+@@ -39,7 +39,6 @@
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PacBioBAM_CXX_FLAGS}")
- # tools
--add_subdirectory(bam2sam)
- add_subdirectory(pbindex)
- add_subdirectory(pbindexdump)
- add_subdirectory(pbmerge)
+ # tools
+- add_subdirectory(bam2sam)
+ add_subdirectory(pbindex)
+ add_subdirectory(pbindexdump)
+ add_subdirectory(pbmerge)
diff --git a/debian/patches/series b/debian/patches/series
index 1989259..78015f5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
-dont-try-building-gtest.patch
ssl-md5.patch
remove-bam2sam.patch
-use-PATH-for-test-programs.patch
diff --git a/debian/patches/use-PATH-for-test-programs.patch b/debian/patches/use-PATH-for-test-programs.patch
deleted file mode 100644
index 0d852d5..0000000
--- a/debian/patches/use-PATH-for-test-programs.patch
+++ /dev/null
@@ -1,125 +0,0 @@
-From 2feac0af36e5d360e74b9e02d5b29901ebabb036 Mon Sep 17 00:00:00 2001
-From: Afif Elghraoui <afif at debian.org>
-Date: Tue, 5 Jul 2016 00:47:08 -0700
-Subject: [PATCH] Rely on PATH to find test programs
-
-Add flexibility to the tests so that they can be used if the
-executables are installed elsewhere rather than fresh out of
-the build tree.
----
- tests/src/cram/bam2sam.t | 4 +++-
- tests/src/cram/pbindexdump_cpp.t | 4 +++-
- tests/src/cram/pbindexdump_json.t | 4 +++-
- tests/src/cram/pbmerge_aligned_ordering.t | 6 +++---
- tests/src/cram/pbmerge_dataset.t | 6 +++---
- tests/src/cram/pbmerge_fofn.t | 6 +++---
- tests/src/cram/pbmerge_mixed_ordering.t | 6 +++---
- tests/src/cram/pbmerge_pacbio_ordering.t | 6 +++---
- 8 files changed, 24 insertions(+), 18 deletions(-)
-
---- pbbam.orig/tests/src/cram/bam2sam.t
-+++ pbbam/tests/src/cram/bam2sam.t
-@@ -1,6 +1,8 @@
- Setup:
-
-- $ BAM2SAM="$TESTDIR/../../../bin/bam2sam" && export BAM2SAM
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+
-+ $ BAM2SAM="bam2sam" && export BAM2SAM
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
-
---- pbbam.orig/tests/src/cram/pbindexdump_cpp.t
-+++ pbbam/tests/src/cram/pbindexdump_cpp.t
-@@ -1,6 +1,8 @@
- Setup:
-
-- $ PBINDEXDUMP="$TESTDIR/../../../bin/pbindexdump" && export PBINDEXDUMP
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+
-+ $ PBINDEXDUMP="pbindexdump" && export PBINDEXDUMP
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
-
---- pbbam.orig/tests/src/cram/pbindexdump_json.t
-+++ pbbam/tests/src/cram/pbindexdump_json.t
-@@ -1,6 +1,8 @@
- Setup:
-
-- $ PBINDEXDUMP="$TESTDIR/../../../bin/pbindexdump" && export PBINDEXDUMP
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+
-+ $ PBINDEXDUMP="pbindexdump" && export PBINDEXDUMP
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
-
---- pbbam.orig/tests/src/cram/pbmerge_aligned_ordering.t
-+++ pbbam/tests/src/cram/pbmerge_aligned_ordering.t
-@@ -1,8 +1,8 @@
- Setup:
-
-- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN
-- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE
-- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+ $ PBMERGE="pbmerge" && export PBMERGE
-+ $ BAM2SAM="bam2sam" && export BAM2SAM
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
- $ INPUT_1="$DATADIR/dataset/bam_mapping_1.bam" && export INPUT_1
---- pbbam.orig/tests/src/cram/pbmerge_dataset.t
-+++ pbbam/tests/src/cram/pbmerge_dataset.t
-@@ -1,8 +1,8 @@
- Setup:
-
-- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN
-- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE
-- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+ $ PBMERGE="pbmerge" && export PBMERGE
-+ $ BAM2SAM="bam2sam" && export BAM2SAM
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
- $ INPUT_XML="$DATADIR/polymerase/consolidate.subread.dataset.xml" && export INPUT_XML
---- pbbam.orig/tests/src/cram/pbmerge_fofn.t
-+++ pbbam/tests/src/cram/pbmerge_fofn.t
-@@ -1,8 +1,8 @@
- Setup:
-
-- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN
-- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE
-- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+ $ PBMERGE="pbmerge" && export PBMERGE
-+ $ BAM2SAM="bam2sam" && export BAM2SAM
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
- $ INPUT_FOFN="$DATADIR/merge.fofn" && export INPUT_FOFN
---- pbbam.orig/tests/src/cram/pbmerge_mixed_ordering.t
-+++ pbbam/tests/src/cram/pbmerge_mixed_ordering.t
-@@ -1,8 +1,8 @@
- Setup:
-
-- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN
-- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE
-- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+ $ PBMERGE="pbmerge" && export PBMERGE
-+ $ BAM2SAM="bam2sam" && export BAM2SAM
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
- $ UNALIGNED_BAM="$DATADIR/polymerase/internal.hqregions.bam" && export UNALIGNED_BAM
---- pbbam.orig/tests/src/cram/pbmerge_pacbio_ordering.t
-+++ pbbam/tests/src/cram/pbmerge_pacbio_ordering.t
-@@ -1,8 +1,8 @@
- Setup:
-
-- $ TOOLS_BIN="$TESTDIR/../../../bin" && export TOOLS_BIN
-- $ PBMERGE="$TOOLS_BIN/pbmerge" && export PBMERGE
-- $ BAM2SAM="$TOOLS_BIN/bam2sam" && export BAM2SAM
-+ $ PATH="$TESTDIR/../../../bin:$PATH" && export PATH
-+ $ PBMERGE="pbmerge" && export PBMERGE
-+ $ BAM2SAM="bam2sam" && export BAM2SAM
-
- $ DATADIR="$TESTDIR/../../data" && export DATADIR
- $ HQREGION_BAM="$DATADIR/polymerase/internal.hqregions.bam" && export HQREGION_BAM
--
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