[med-svn] [pbbam] 03/11: Configure autopkgtests
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 5 11:05:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository pbbam.
commit bed07808f5e3bcec2dd88a0f843f2879d5ac9d52
Author: Afif Elghraoui <afif at debian.org>
Date: Tue Jul 5 02:38:51 2016 -0700
Configure autopkgtests
---
debian/patches/series | 1 +
debian/patches/use-PATH-for-test-programs.patch | 125 ++++++++++++++++++++++++
debian/tests/control | 7 ++
debian/tests/pbbamtools | 8 ++
4 files changed, 141 insertions(+)
diff --git a/debian/patches/series b/debian/patches/series
index c87ab09..1989259 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
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
new file mode 100644
index 0000000..1b6c1b7
--- /dev/null
+++ b/debian/patches/use-PATH-for-test-programs.patch
@@ -0,0 +1,125 @@
+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/dataset/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
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..25b6960
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,7 @@
+Tests: pbbamtools
+Depends:
+ make,
+ pbbamtools,
+ python-cram,
+Restrictions:
+ needs-recommends,
diff --git a/debian/tests/pbbamtools b/debian/tests/pbbamtools
new file mode 100755
index 0000000..87c7c22
--- /dev/null
+++ b/debian/tests/pbbamtools
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+cp -r tests $ADTTMP
+
+make -f debian/rules \
+ $(ls $ADTTMP/tests/src/cram/pb*.t | sed 's/\.t$/.deb.t/')
+
+cd $ADTTMP && cram -v tests/src/cram/*.deb.t
--
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