sample_data/test_DE_analysis/Makefile | 9 7 + 2 - 0 !
1 file changed, 7 insertions(+), 2 deletions(-)

 skip tests for kallisto & deseq2 programs; not currently packaged for
Debian

Trinity | 26 0 + 26 - 0 !
1 file changed, 26 deletions(-)

 don't try to test java

Trinity | 2 1 + 1 - 0 !
util/insilico_read_normalization.pl | 2 1 + 1 - 0 !
util/misc/run_jellyfish.pl | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

jellyfish path

Chrysalis/analysis/Chrysalis.cc | 2 1 + 1 - 0 !
Trinity | 12 6 + 6 - 0 !
2 files changed, 7 insertions(+), 7 deletions(-)

 updates the main trinity program to use fhs paths

Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 compatibility fix due to use of newer libcommons-collections4-java

Inchworm/src/sequenceUtil.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix_istream_failure_call

Upstream is using wrong test gor file open failure, comparing an int instead
of calling fail() method

Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl | 2 1 + 1 - 0 !
Trinity | 7 3 + 4 - 0 !
util/align_and_estimate_abundance.pl | 9 4 + 5 - 0 !
3 files changed, 8 insertions(+), 10 deletions(-)

 drop some use of findbin and hardcode paths

Trinity | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 disable the version "phone home" for privacy

Trinity | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 match the debian's path

Chrysalis/Makefile | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 fix building with gcc 6
 Upstream handles GCC versions separately in their Makefile
 but didn't consider version 6. Cloning settings for GCC 5 to use
 with GCC 6, works.