[med-svn] [trinityrnaseq] branch upstream updated (f018d02 -> 1a1969d)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Feb 12 22:38:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository trinityrnaseq.
from f018d02 Imported Upstream version 2.0.2
new 1a1969d Imported Upstream version 2.0.3+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
Butterfly/Butterfly.jar | Bin 1426909 -> 1427334 bytes
Butterfly/src/lib/Jaligner.jar | Bin 266463 -> 0 bytes
Butterfly/src/lib/collections-generic-4.01.jar | Bin 531557 -> 0 bytes
Butterfly/src/lib/java-getopt-1.0.13.jar | Bin 56709 -> 0 bytes
Butterfly/src/lib/jung-algorithms-2.0.1.jar | Bin 233113 -> 0 bytes
Butterfly/src/lib/jung-api-2.0.1.jar | Bin 40975 -> 0 bytes
Butterfly/src/lib/jung-graph-impl-2.0.1.jar | Bin 62329 -> 0 bytes
Butterfly/src/src/SeqVertex.java | 1 +
Butterfly/src/src/TransAssembly_allProbPaths.java | 71 +++-
Chrysalis/analysis/ReadsToTranscripts.cc | 2 +-
Makefile | 8 +-
PerlLib/{HTC => HPC}/Base_handler.pm | 2 +-
PerlLib/{HTC => HPC}/FarmIt.pm | 4 +-
PerlLib/{HTC => HPC}/GridRunner.pm | 93 +++--
PerlLib/{HTC => HPC}/LSF_handler.pm | 4 +-
PerlLib/{HTC => HPC}/PBS_handler.pm | 4 +-
PerlLib/{HTC => HPC}/SGE_handler.pm | 4 +-
PerlLib/{HTC => HPC}/SLURM_handler.pm | 4 +-
PerlLib/Pipeliner.pm | 11 +-
Release.Notes | 16 +
Trinity | 406 +++++++++++++++------
..._edgeR.xml => EdgeR_differentialExpression.xml} | 8 +-
...trix.xml => abundance_estimation_to_matrix.xml} | 21 +-
.../abundance_estimation_to_matrix_wrapper.py | 40 ++
{htc_conf => hpc_conf}/BroadInst_LSF.hour.10.conf | 0
.../BroadInst_LSF.neurolab.1.conf | 0
.../BroadInst_LSF.neurolab.10.conf | 0
.../BroadInst_LSF.neurolab.100.conf | 0
{htc_conf => hpc_conf}/BroadInst_LSF.regev.1.conf | 0
{htc_conf => hpc_conf}/BroadInst_LSF.regev.10.conf | 0
.../BroadInst_LSF.regev.100.conf | 0
{htc_conf => hpc_conf}/BroadInst_LSF.test.conf | 0
{htc_conf => hpc_conf}/BroadInst_LSF.week.1.conf | 0
{htc_conf => hpc_conf}/BroadInst_SGE.test.conf | 0
{htc_conf => hpc_conf}/PBS.test.conf | 0
{htc_conf => hpc_conf}/SLURM.test.conf | 0
.../deprecated/BroadInst_LSF.Trinity.conf | 0
.../deprecated/BroadInst_LSF.blast.conf | 0
.../deprecated/BroadInst_LSF.conf | 0
.../deprecated/BroadInst_LSF.regev.10.conf | 0
.../deprecated/BroadInst_LSF.regev.100.conf | 0
.../deprecated/BroadInst_LSF.regev.1000.conf | 0
.../deprecated/BroadInst_LSF.test.conf | 0
.../deprecated/BroadInst_SGE.conf | 0
.../deprecated/BroadInst_SGE.test.conf | 0
{htc_conf => hpc_conf}/deprecated/SLURM.FAS.conf | 0
trinity-plugins/Makefile | 43 ++-
trinity-plugins/Trimmomatic | 1 -
trinity-plugins/collectl/make_data_files.py | 17 +-
trinity-plugins/fastool | 1 -
trinity-plugins/jellyfish-2.1.4.tar.gz | Bin 958038 -> 0 bytes
trinity-plugins/parafly | 1 -
.../{parafly-r2013-01-21 => parafly-code}/LICENSE | 0
.../Makefile.am | 0
.../Makefile.in | 0
.../aclocal.m4 | 0
.../{parafly-r2013-01-21 => parafly-code}/config.h | 0
.../config.h.in | 0
.../configure | 0
.../configure.ac | 0
.../{parafly-r2013-01-21 => parafly-code}/depcomp | 0
.../install-sh | 0
.../{parafly-r2013-01-21 => parafly-code}/missing | 0
.../src/Makefile.am | 0
.../src/Makefile.in | 0
.../src/ParaFly.cpp | 10 +-
.../src/argProcessor.cpp | 0
.../src/argProcessor.hpp | 0
.../{parafly-r2013-01-21 => parafly-code}/stamp-h1 | 0
util/HTC_helpers/bsub_fasta_bin_cmd_processor.pl | 201 ----------
util/HTC_helpers/get_failed_cmds.pl | 48 ---
util/HTC_helpers/htc_bin_blastPlus.pl | 224 ------------
util/HTC_helpers/run_cmds_on_grid.pl | 92 -----
util/support_scripts/ExitTester.jar | Bin 8259 -> 0 bytes
.../get_Trinity_gene_to_trans_map.pl | 2 +-
.../partition_chrysalis_graphs_n_reads.pl | 2 +-
util/support_scripts/tests.py | 40 +-
77 files changed, 582 insertions(+), 799 deletions(-)
delete mode 100644 Butterfly/src/lib/Jaligner.jar
delete mode 100755 Butterfly/src/lib/collections-generic-4.01.jar
delete mode 100644 Butterfly/src/lib/java-getopt-1.0.13.jar
delete mode 100755 Butterfly/src/lib/jung-algorithms-2.0.1.jar
delete mode 100755 Butterfly/src/lib/jung-api-2.0.1.jar
delete mode 100755 Butterfly/src/lib/jung-graph-impl-2.0.1.jar
rename PerlLib/{HTC => HPC}/Base_handler.pm (98%)
rename PerlLib/{HTC => HPC}/FarmIt.pm (99%)
mode change 100755 => 100644
rename PerlLib/{HTC => HPC}/GridRunner.pm (66%)
rename PerlLib/{HTC => HPC}/LSF_handler.pm (97%)
rename PerlLib/{HTC => HPC}/PBS_handler.pm (93%)
rename PerlLib/{HTC => HPC}/SGE_handler.pm (97%)
rename PerlLib/{HTC => HPC}/SLURM_handler.pm (93%)
copy galaxy-plugin/{diffExpress_edgeR.xml => EdgeR_differentialExpression.xml} (85%)
copy galaxy-plugin/{RSEM_estimates_to_matrix.xml => abundance_estimation_to_matrix.xml} (68%)
create mode 100644 galaxy-plugin/abundance_estimation_to_matrix_wrapper.py
rename {htc_conf => hpc_conf}/BroadInst_LSF.hour.10.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.neurolab.1.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.neurolab.10.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.neurolab.100.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.regev.1.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.regev.10.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.regev.100.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.test.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_LSF.week.1.conf (100%)
rename {htc_conf => hpc_conf}/BroadInst_SGE.test.conf (100%)
rename {htc_conf => hpc_conf}/PBS.test.conf (100%)
rename {htc_conf => hpc_conf}/SLURM.test.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_LSF.Trinity.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_LSF.blast.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_LSF.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_LSF.regev.10.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_LSF.regev.100.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_LSF.regev.1000.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_LSF.test.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_SGE.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/BroadInst_SGE.test.conf (100%)
rename {htc_conf => hpc_conf}/deprecated/SLURM.FAS.conf (100%)
delete mode 120000 trinity-plugins/Trimmomatic
delete mode 120000 trinity-plugins/fastool
delete mode 100644 trinity-plugins/jellyfish-2.1.4.tar.gz
delete mode 120000 trinity-plugins/parafly
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/LICENSE (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/Makefile.am (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/Makefile.in (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/aclocal.m4 (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/config.h (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/config.h.in (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/configure (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/configure.ac (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/depcomp (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/install-sh (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/missing (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/src/Makefile.am (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/src/Makefile.in (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/src/ParaFly.cpp (94%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/src/argProcessor.cpp (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/src/argProcessor.hpp (100%)
rename trinity-plugins/{parafly-r2013-01-21 => parafly-code}/stamp-h1 (100%)
delete mode 100755 util/HTC_helpers/bsub_fasta_bin_cmd_processor.pl
delete mode 100755 util/HTC_helpers/get_failed_cmds.pl
delete mode 100755 util/HTC_helpers/htc_bin_blastPlus.pl
delete mode 100755 util/HTC_helpers/run_cmds_on_grid.pl
delete mode 100644 util/support_scripts/ExitTester.jar
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