Package: sra-sdk / 2.8.1-2+dfsg-2~bpo8+1

Metadata

Package Version Patches format
sra-sdk 2.8.1-2+dfsg-2~bpo8+1 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
find_configure_libs.patch | (download)

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

 help configure finding debian packaged libraries


10_portability.patch | (download)

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


hardening.patch | (download)

Makefile | 6 3 + 3 - 0 !
build/Makefile.env | 4 2 + 2 - 0 !
2 files changed, 5 insertions(+), 5 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


find_hdf5_serial.patch | (download)

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


find_ngs sdk.patch | (download)

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


find_ncbi vdb.patch | (download)

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


link_debian_packaged_libz.patch | (download)

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


link_debian_packaged_lmagic.patch | (download)

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

 link against debian packages libmagic


dont_use_static_lib.patch | (download)

test/fuse/Makefile | 2 1 + 1 - 0 !
test/general-loader/Makefile | 4 2 + 2 - 0 !
test/ngs-pileup/Makefile | 2 1 + 1 - 0 !
tools/fastq-dump/Makefile | 2 1 + 1 - 0 !
tools/general-loader/Makefile | 2 1 + 1 - 0 !
tools/ngs-pileup/Makefile | 2 1 + 1 - 0 !
tools/pileup-stats/Makefile | 2 1 + 1 - 0 !
tools/sra-seq-count/Makefile | 2 1 + 1 - 0 !
8 files changed, 9 insertions(+), 9 deletions(-)

 don't use static library


set_explicit_path_to_schemata.patch | (download)

test/fastq-loader/test-fastq-loader.cpp | 2 1 + 1 - 0 !
test/general-loader/makeinputs.cpp | 12 6 + 6 - 0 !
test/general-loader/test-general-loader.cpp | 4 2 + 2 - 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 !
10 files changed, 20 insertions(+), 20 deletions(-)

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


absolute_vschema_path_in_test.patch | (download)

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

 we need to set absolute pathes also in the test
ignore_failing_tests_for_the_moment.patch | (download)

test/Makefile | 2 1 + 1 - 0 !
test/fastq-loader/Makefile | 18 9 + 9 - 0 !
2 files changed, 10 insertions(+), 10 deletions(-)

 exclude failing tests


do_not_link_statically.patch | (download)

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

 do not link statically


link_debian_packaged_libmbed.patch | (download)

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

 link against debian packaged libmbedtls-dev


seek_dynamic_libs.patch | (download)

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


certs.kfg.patch | (download)

build/Makefile.env | 4 2 + 2 - 0 !
build/Makefile.install | 1 1 + 0 - 0 !
2 files changed, 3 insertions(+), 2 deletions(-)

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


jessie_force_fPIC.patch | (download)

tools/align-cache/Makefile | 2 2 + 0 - 0 !
tools/bam-loader/Makefile | 2 2 + 0 - 0 !
tools/general-loader/Makefile | 2 2 + 0 - 0 !
tools/pileup-stats/Makefile | 2 2 + 0 - 0 !
tools/vdb-config/Makefile | 2 2 + 0 - 0 !
tools/vdb-validate/Makefile | 4 3 + 1 - 0 !
6 files changed, 13 insertions(+), 1 deletion(-)

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