Commit da2a7765 authored by Shayan Doust's avatar Shayan Doust
Browse files

Autopkgtest now works using pre-existing test scripts

parent b4a3a065

CMakeLists.txt

+10 −7
Original line number Diff line number Diff line
@@ -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 → 100644
+92 −0
Original line number Diff line number Diff line 
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 −0
Original line number Diff line number Diff line 
use_debian_packaged_gatb-core.patch

remove_unnecessary_installs.patch

modify_tests_for_autopkgtest.patch

debian/tests/run-unit-test

+8 −3
Original line number Diff line number Diff line 
#!/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

+3 −16
Original line number Diff line number Diff line 
#! /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