tests/bedops/Makefile | 2 1 + 1 - 0 !
tests/starch/Makefile | 14 7 + 7 - 0 !
2 files changed, 8 insertions(+), 8 deletions(-)

 use the installed binaries instead of the locally generated ones

applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py | 4 2 + 2 - 0 !
applications/bed/sort-bed/src/update-sort-bed-slurm.py | 4 2 + 2 - 0 !
applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py | 4 2 + 2 - 0 !
applications/bed/starch/src/starch-diff.py | 10 5 + 5 - 0 !
applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py | 12 6 + 6 - 0 !
applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py | 12 6 + 6 - 0 !
applications/bed/starch/test/unsortable_elements/src/isUnsortable.py | 2 1 + 1 - 0 !
docs/conf.py | 24 12 + 12 - 0 !
tests/starch/generate_random_intervals.sh | 10 5 + 5 - 0 !
9 files changed, 41 insertions(+), 41 deletions(-)

 port python files using python2 to python3

applications/bed/bedextract/src/Makefile | 8 4 + 4 - 0 !
applications/bed/bedmap/src/Makefile | 8 4 + 4 - 0 !
applications/bed/bedops/src/Makefile | 8 4 + 4 - 0 !
applications/bed/closestfeats/src/Makefile | 8 4 + 4 - 0 !
applications/bed/conversion/src/Makefile | 2 1 + 1 - 0 !
applications/bed/sort-bed/src/Makefile | 8 4 + 4 - 0 !
applications/bed/starch/src/Makefile | 10 5 + 5 - 0 !
docs/conf.py | 9 4 + 5 - 0 !
system.mk/Makefile.linux | 18 9 + 9 - 0 !
9 files changed, 39 insertions(+), 40 deletions(-)

 upstream makes use of embedded libs, use debian ones.

Makefile | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 let gnu make jobserver handle parallel make jobs.
 dh calls toplevel make with a suitable "-j", so let's not override that.

docs/conf.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 add patch to adapt to newer sphinx api

docs/conf.py | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 remove intersphinx, it is unneeded and in the wrong format