setup/konfigure.perl | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 help configure finding debian packaged libraries

build/Makefile.shell | 24 11 + 13 - 0 !
1 file changed, 11 insertions(+), 13 deletions(-)

 drop redundant -m32/-m64 option to enable build
             on all Debian architectures

Makefile | 6 3 + 3 - 0 !
build/Makefile.env | 6 3 + 3 - 0 !
2 files changed, 6 insertions(+), 6 deletions(-)

 propagate debian hardening options into build system
  This is most probably not the most elegant way, but when simply
  setting CFLAGS in debian/rules they simply override the CFLAGS
  setting inside the sequence of Makefiles which leads to a loss of
  DEFINES and INCDIRS which are needed to build properly

setup/konfigure.perl | 2 1 + 1 - 0 !
tools/pacbio-load/Makefile | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 debian has several flavours of hdf5 - use serial here

setup/konfigure.perl | 7 5 + 2 - 0 !
setup/package.prl | 4 2 + 2 - 0 !
2 files changed, 7 insertions(+), 4 deletions(-)

 ngs-sdk header files are in /usr/include

setup/konfigure.perl | 5 4 + 1 - 0 !
setup/package.prl | 8 4 + 4 - 0 !
2 files changed, 8 insertions(+), 5 deletions(-)

 make sure libncbi-vdb will be found

build/ld.linux.exe.sh | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 since libncbi-vdb is dynamically linked against zlib and libbz2
 these need to be explicitly specified here

tools/copycat/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 link against debian packages libmagic

test/fuse/Makefile | 2 1 + 1 - 0 !
test/ngs-pileup/Makefile | 2 1 + 1 - 0 !
tools/fastq-dump/Makefile | 2 1 + 1 - 0 !
tools/ngs-pileup/Makefile | 2 1 + 1 - 0 !
tools/sra-seq-count/Makefile | 2 1 + 1 - 0 !
5 files changed, 5 insertions(+), 5 deletions(-)

 don't use static library

test/fastq-loader/test-fastq-loader.cpp | 2 1 + 1 - 0 !
tools/bam-loader/bam-loader.c | 2 1 + 1 - 0 !
tools/cg-load/cg-load.c | 2 1 + 1 - 0 !
tools/fastq-loader/fastq-loader.c | 2 1 + 1 - 0 !
tools/pacbio-load/pl-context.h | 2 1 + 1 - 0 !
tools/sra-sort/run.c | 2 1 + 1 - 0 !
tools/util/sortreadtest.c | 4 2 + 2 - 0 !
tools/vdb-copy/vdb-copy.kfg | 8 4 + 4 - 0 !
8 files changed, 12 insertions(+), 12 deletions(-)

 in debian */*.vschema is installed to /usr/lib/ncbi-vdb/

test/vcf-loader/test-vcf-loader.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 we need to set absolute paths also in the test

test/Makefile | 1 0 + 1 - 0 !
test/fastq-loader/Makefile | 16 8 + 8 - 0 !
2 files changed, 8 insertions(+), 9 deletions(-)

 exclude failing tests

build/ld.linux.gcc.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 do not link statically

build/ld.linux.exe.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 link against debian packaged libmbedtls-dev

setup/package.prl | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 seek for dynamic lib rather than static if dynamic lib exists

build/Makefile.env | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 point to correct location of kfg config files in libncbi-vdb2 package

test/Makefile | 2 0 + 2 - 0 !
test/sra-pileup/Makefile | 2 1 + 1 - 0 !
2 files changed, 1 insertion(+), 3 deletions(-)

 drop tests that require network access

test/Makefile | 10 2 + 8 - 0 !
1 file changed, 2 insertions(+), 8 deletions(-)

 it needs to be investigated why this test is failing with:
 align-cache:
 .
 /build/sra-sdk-2.9.0+dfsg/test/align-cache# /build/sra-sdk-2.9.0+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/align-cache -t 10 --min-cache-count 1 CSRA_file CSRA_file.cache
 2018-03-24T08:35:56 align-cache.2.9.0 err: VSchemaParseFile (align/mate-cache.vschema) failed with code 0x31c50918 (834996504) [RC(libs/vdb/schema.c:858:VSchemaOpenFile rcFS,rcDirectory,rcOpening,rcPath,rcNotFound)]
 .
 .
 copycat:
 .
 /build/sra-sdk-2.9.0+dfsg/test/copycat# make
 Starting copycat tests...
 2018-03-24T08:48:48 copycat.2.9.0 int: libs/kfs/ffmagic.c:943:KMagicFileFormatMake: loadable library unexpected while loading file format within file format detection module - failed to create file format

build/gprof2dot.py | 134 68 + 66 - 0 !
setup/install.perl | 2 1 + 1 - 0 !
test/dbgap-mount/py/test/__init__.py | 6 3 + 3 - 0 !
test/dbgap-mount/py/test/test.py | 4 2 + 2 - 0 !
test/samline/bx_tag_test.py | 4 2 + 2 - 0 !
test/samline/ca_test.py | 28 14 + 14 - 0 !
test/samline/sam.py | 16 8 + 8 - 0 !
test/sra-pileup/check_skiplist.py | 2 1 + 1 - 0 !
test/sra-pileup/test_all_sam_dump_has_spotgroup.py | 2 1 + 1 - 0 !
test/sra-pileup/test_diff_fastq_dump_vs_sam_dump.py | 2 1 + 1 - 0 !
test/tarballs/test-tarballs.sh | 2 1 + 1 - 0 !
tools/fasterq-dump/fastq-diff.py | 6 3 + 3 - 0 !
12 files changed, 105 insertions(+), 103 deletions(-)

 upgrade from python2 to python 3

tools/util/validate-names4.c | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

---

tools/driver-tool/tool-path.hpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---

build/Makefile.install | 2 1 + 1 - 0 !
tools/Makefile | 1 0 + 1 - 0 !
2 files changed, 1 insertion(+), 2 deletions(-)

---