[med-svn] [trinityrnaseq] branch master updated (8e8f11d -> cb9cc22)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Feb 12 22:37:12 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository trinityrnaseq.
from 8e8f11d In some cases help2man has poor results - here it was the case. So I did some (boring) manual editing
new 9dec0c1 add watch; properly exclude files
new e279efe Imported Upstream version 2.0.3+dfsg
new cb9cc22 bump version & clarify copyrights
The 3 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 +++++++++++++++------
debian/changelog | 2 +-
debian/control | 4 +-
debian/copyright | 22 +-
debian/patches/chrysalis-makefile-auto | 212 -----------
debian/patches/jellyfish-path | 2 +-
debian/patches/noExitTester | 8 +-
debian/patches/series | 1 -
debian/rules | 5 +-
debian/watch | 33 +-
..._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 +-
86 files changed, 612 insertions(+), 1058 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%)
delete mode 100644 debian/patches/chrysalis-makefile-auto
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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