[med-svn] [Git][med-team/mindthegap][master] Autopkgtest now works using pre-existing test scripts
Shayan Doust
gitlab at salsa.debian.org
Tue Jul 9 15:18:36 BST 2019
Shayan Doust pushed to branch master at Debian Med / mindthegap
Commits:
da2a7765 by Shayan Doust at 2019-07-09T04:47:07Z
Autopkgtest now works using pre-existing test scripts
- - - - -
6 changed files:
- CMakeLists.txt
- + debian/patches/modify_tests_for_autopkgtest.patch
- debian/patches/series
- debian/tests/run-unit-test
- test/simple_full_test.sh
- test/simple_test.sh
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -71,7 +71,7 @@ SET (GATB_CORE_EXCLUDE_TESTS 1)
SET (GATB_CORE_EXCLUDE_EXAMPLES 1)
# GATB CORE
-include (GatbCore)
+# include (GatbCore)
################################################################################
# TOOL
@@ -106,11 +106,14 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
# we define the files to be compiled
file (GLOB_RECURSE ProjectFiles src/*)
+include(GNUInstallDirs)
+LINK_DIRECTORIES ( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
+
# we define the artifact to be built: the project binary
add_executable (${PROJECT_NAME} src/main.cpp ${ProjectFiles})
# we define which libraries to be linked with project binary
-target_link_libraries (${PROJECT_NAME} ${gatb-core-libraries})
+target_link_libraries (${PROJECT_NAME} gatbcore hdf5)
################################################################################
@@ -145,12 +148,12 @@ SET (CPACK_SOURCE_IGNORE_FILES
# We copy the project binary to the 'bin' directory
INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test DESTINATION .)
-INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data DESTINATION .)
+#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test DESTINATION .)
+#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data DESTINATION .)
#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc DESTINATION .)
-INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.md DESTINATION .)
-INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.md DESTINATION .)
-INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION .)
+#INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.md DESTINATION .)
+#INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.md DESTINATION .)
+#INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION .)
# We include the "bin" tag into binary archive file name
set (CPACK_PACKAGE_FILE_NAME ${PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME})
=====================================
debian/patches/modify_tests_for_autopkgtest.patch
=====================================
@@ -0,0 +1,92 @@
+Index: mindthegap/test/simple_full_test.sh
+===================================================================
+--- mindthegap.orig/test/simple_full_test.sh
++++ mindthegap/test/simple_full_test.sh
+@@ -1,18 +1,5 @@
+ #! /bin/bash
+
+-# look for MindTheGap binary. In devel mode, it's in ../build/bin directory.
+-# In production mode, it's in ../bin directory.
+-if [ -f "../bin/MindTheGap" ]
+-then
+- bindir="../bin"
+-elif [ -f "../build/bin/MindTheGap" ]
+-then
+- bindir="../build/bin"
+-else
+- echo "could not find a compiled MindTheGap binary"
+- exit 1
+-fi
+-
+ RETVAL=0
+ testDir="test-output"
+ outputPrefix=$testDir/full-test
+@@ -33,7 +20,7 @@ mkdir $testDir
+ ################################################################################
+ # we launch the find module
+ ################################################################################
+-${bindir}/MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1 2> /dev/null
++MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1 2> /dev/null
+
+ ################################################################################
+ # we check the results
+@@ -78,7 +65,7 @@ fi
+ ################################################################################
+ # we launch the fill module
+ ################################################################################
+-${bindir}/MindTheGap fill -graph $outputPrefix.h5 -bkpt $outputPrefix.breakpoints -out $outputPrefix -nb-cores 1 >>$outputPrefix.out 2> /dev/null
++MindTheGap fill -graph $outputPrefix.h5 -bkpt $outputPrefix.breakpoints -out $outputPrefix -nb-cores 1 >>$outputPrefix.out 2> /dev/null
+
+ ################################################################################
+ # we check the results
+@@ -117,7 +104,7 @@ fi
+ ################################################################################
+ # we launch the fill module in contig mode
+ ################################################################################
+-${bindir}/MindTheGap fill -in ../data/contig-reads.fasta.gz -contig ../data/contigs.fasta -abundance-min 3 -out $outputPrefix2 -nb-cores 1 >>$outputPrefix2.out 2> /dev/null
++MindTheGap fill -in ../data/contig-reads.fasta.gz -contig ../data/contigs.fasta -abundance-min 3 -out $outputPrefix2 -nb-cores 1 >>$outputPrefix2.out 2> /dev/null
+
+ ################################################################################
+ # we check the results
+Index: mindthegap/test/simple_test.sh
+===================================================================
+--- mindthegap.orig/test/simple_test.sh
++++ mindthegap/test/simple_test.sh
+@@ -1,26 +1,13 @@
+ #!/bin/bash
+
+-# look for MindTheGap binary. In devel mode, it's in ../build/bin directory.
+-# In production mode, it's in ../bin directory.
+-if [ -f "../bin/MindTheGap" ]
+-then
+- bindir="../bin"
+-elif [ -f "../build/bin/MindTheGap" ]
+-then
+- bindir="../build/bin"
+-else
+- echo "could not find a compiled mindthegap binary"
+- exit 1
+-fi
+-
+ testOK="true"
+
+ run_test()
+ {
+ # param : reads_file ref_file true_result prefix
+- $bindir/MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
++ MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
+
+- $bindir/MindTheGap fill -bkpt output/$4_find.breakpoints -graph output/$4_find.h5 -out output/$4_fill 1> output/$4_fill.out 2> output/$4_fill.err
++ MindTheGap fill -bkpt output/$4_find.breakpoints -graph output/$4_find.h5 -out output/$4_fill 1> output/$4_fill.out 2> output/$4_fill.err
+
+ tmp1=output/$4_fill.insertions.fasta.tmp
+ tmp2=output/tmp2
+@@ -45,7 +32,7 @@ run_test()
+ run_test_vcf()
+ {
+ # param : reads_file ref_file true_result prefix
+- $bindir/MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
++ MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
+
+ sh compare_vcf.sh output/$4_find.othervariants.vcf $3 1> /dev/null 2>&1
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
use_debian_packaged_gatb-core.patch
remove_unnecessary_installs.patch
+modify_tests_for_autopkgtest.patch
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
set -e
-pkg=#PACKAGENAME#
+pkg=mindthegap
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
@@ -11,8 +11,13 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+cp -r /usr/share/mindthegap/test "${AUTOPKGTEST_TMP}"
+cp -r /usr/share/mindthegap/data "${AUTOPKGTEST_TMP}"
-cd "${AUTOPKGTEST_TMP}"
+cd "${AUTOPKGTEST_TMP}"/test
#do_stuff_to_test_package#
+echo "Invoking simple_test.sh:"
+bash simple_test.sh
+echo "Invoking simple_full_test.sh:"
+bash simple_full_test.sh
=====================================
test/simple_full_test.sh
=====================================
@@ -1,18 +1,5 @@
#! /bin/bash
-# look for MindTheGap binary. In devel mode, it's in ../build/bin directory.
-# In production mode, it's in ../bin directory.
-if [ -f "../bin/MindTheGap" ]
-then
- bindir="../bin"
-elif [ -f "../build/bin/MindTheGap" ]
-then
- bindir="../build/bin"
-else
- echo "could not find a compiled MindTheGap binary"
- exit 1
-fi
-
RETVAL=0
testDir="test-output"
outputPrefix=$testDir/full-test
@@ -33,7 +20,7 @@ mkdir $testDir
################################################################################
# we launch the find module
################################################################################
-${bindir}/MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1 2> /dev/null
+MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref ../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1 2> /dev/null
################################################################################
# we check the results
@@ -78,7 +65,7 @@ fi
################################################################################
# we launch the fill module
################################################################################
-${bindir}/MindTheGap fill -graph $outputPrefix.h5 -bkpt $outputPrefix.breakpoints -out $outputPrefix -nb-cores 1 >>$outputPrefix.out 2> /dev/null
+MindTheGap fill -graph $outputPrefix.h5 -bkpt $outputPrefix.breakpoints -out $outputPrefix -nb-cores 1 >>$outputPrefix.out 2> /dev/null
################################################################################
# we check the results
@@ -117,7 +104,7 @@ fi
################################################################################
# we launch the fill module in contig mode
################################################################################
-${bindir}/MindTheGap fill -in ../data/contig-reads.fasta.gz -contig ../data/contigs.fasta -abundance-min 3 -out $outputPrefix2 -nb-cores 1 >>$outputPrefix2.out 2> /dev/null
+MindTheGap fill -in ../data/contig-reads.fasta.gz -contig ../data/contigs.fasta -abundance-min 3 -out $outputPrefix2 -nb-cores 1 >>$outputPrefix2.out 2> /dev/null
################################################################################
# we check the results
=====================================
test/simple_test.sh
=====================================
@@ -1,26 +1,13 @@
#!/bin/bash
-# look for MindTheGap binary. In devel mode, it's in ../build/bin directory.
-# In production mode, it's in ../bin directory.
-if [ -f "../bin/MindTheGap" ]
-then
- bindir="../bin"
-elif [ -f "../build/bin/MindTheGap" ]
-then
- bindir="../build/bin"
-else
- echo "could not find a compiled mindthegap binary"
- exit 1
-fi
-
testOK="true"
run_test()
{
# param : reads_file ref_file true_result prefix
- $bindir/MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
+ MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
- $bindir/MindTheGap fill -bkpt output/$4_find.breakpoints -graph output/$4_find.h5 -out output/$4_fill 1> output/$4_fill.out 2> output/$4_fill.err
+ MindTheGap fill -bkpt output/$4_find.breakpoints -graph output/$4_find.h5 -out output/$4_fill 1> output/$4_fill.out 2> output/$4_fill.err
tmp1=output/$4_fill.insertions.fasta.tmp
tmp2=output/tmp2
@@ -45,7 +32,7 @@ run_test()
run_test_vcf()
{
# param : reads_file ref_file true_result prefix
- $bindir/MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
+ MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
sh compare_vcf.sh output/$4_find.othervariants.vcf $3 1> /dev/null 2>&1
View it on GitLab: https://salsa.debian.org/med-team/mindthegap/commit/da2a77652843afbd7526dd8230045a4e01f6ec76
--
View it on GitLab: https://salsa.debian.org/med-team/mindthegap/commit/da2a77652843afbd7526dd8230045a4e01f6ec76
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