trinity-plugins/Makefile | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 skip cleaning parafly, we don't build it here

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

 don't try to test java

util/misc/run_jellyfish.pl | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

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 | 6 6 + 0 - 0 !
1 file changed, 6 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.
 Same for gcc 7 (Gert Wollny, <gewo@debian.org>

Butterfly/src/src/NWalign.java | 2 1 + 1 - 0 !
Butterfly/src/src/NeedlemanWunschGotohBanded.java | 493 493 + 0 - 0 !
2 files changed, 494 insertions(+), 1 deletion(-)

---

Chrysalis/Makefile_g++_i386 | 2 1 + 1 - 0 !
Chrysalis/Makefile_g++_i686 | 2 1 + 1 - 0 !
Chrysalis/Makefile_g++_i86pc | 2 1 + 1 - 0 !
Chrysalis/Makefile_g++_x86_64 | 2 1 + 1 - 0 !
Chrysalis/Makefile_g++_x86_64_mpi | 2 1 + 1 - 0 !
5 files changed, 5 insertions(+), 5 deletions(-)

 starting with glibc 2.27, support for the "ieee" library (part of
 SVID specification) has been removed. The libieee.a library is therefore not
 shipped anymore. In the trinityrnaseq case, GCC tries to link with this
 library due to the use of the -mieee-fp option. Removing this option
 from the Makefile is enough to fix the issue. This is what the patch does.

Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/extract_supertranscript_from_reference.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Compact_graph_partial.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Compact_graph_whole.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/DP_matrix.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/GraphCycleException.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Node_alignment.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Node_path.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Splice_model_refiner.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/TGLOBALS.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/TGraph.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/TNode.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Topological_sort.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Trinity_util.py | 2 1 + 1 - 0 !
PyLib/Pipeliner.py | 2 1 + 1 - 0 !
trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py | 2 1 + 1 - 0 !
trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py | 2 1 + 1 - 0 !
util/misc/TPM_weighted_gene_length.py | 2 1 + 1 - 0 !
util/support_scripts/trinity_installer.py | 2 1 + 1 - 0 !
22 files changed, 22 insertions(+), 22 deletions(-)

 default to running python 3

Trinity | 37 23 + 14 - 0 !
1 file changed, 23 insertions(+), 14 deletions(-)

 use updated java version check from upstream

sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_as_DS.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_bowtie_components.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_full_cleanup.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_cleanup.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_parallel_iworm_assembly.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_piecemeal.sh | 10 6 + 4 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_trin_complete.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_bowtie2.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_my_ramdisk.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_LSF.sh | 4 1 + 3 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe.singleFQ.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_NO_normalization.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_docker.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_lenient_path_extension.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/runMe.sh | 4 3 + 1 - 0 !
26 files changed, 74 insertions(+), 36 deletions(-)

 don't hardcode number of --cpu (especially above 2)

blastn -num_threads will not accept a number larger than the cores/CPUs it
detects and will exit with an error. Some Debian test (virtual) machines only
have two cores and thus they failed our testing.

With this patch we detect in a unix/macOS friendly way the number of cores
using `nproc` or `sysctl -n hw.physicalcpu` (respectively). Thus execution of
the sample_data tests will be much faster for most developers/users.

Perhaps Trinity itself could be taught this trick and the --CPU option would
not be needed by default.