[med-svn] [trinityrnaseq] 03/03: bump version & clarify copyrights
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 commit to branch master
in repository trinityrnaseq.
commit cb9cc222e4afa4ac775d08cb6f753ff99a1c6125
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Thu Feb 12 14:04:52 2015 -0500
bump version & clarify copyrights
---
debian/changelog | 2 +-
debian/control | 4 +-
debian/copyright | 20 +++-
debian/patches/chrysalis-makefile-auto | 212 ---------------------------------
debian/patches/jellyfish-path | 2 +-
debian/patches/noExitTester | 8 +-
debian/patches/series | 1 -
debian/rules | 5 +-
8 files changed, 28 insertions(+), 226 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 04082c0..e3212aa 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-trinityrnaseq (2.0.2-1) UNRELEASED; urgency=low
+trinityrnaseq (2.0.3+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #777697)
diff --git a/debian/control b/debian/control
index 33bd4c7..4cc931d 100644
--- a/debian/control
+++ b/debian/control
@@ -29,7 +29,9 @@ Depends: ${shlibs:Depends},
r-base-core,
r-bioc-edger,
rsem,
- express
+ express,
+ trimmomatic,
+Suggests: collectl
Description: RNA-Seq De novo Assembly
Trinity represents a novel method for the efficient and robust de novo
reconstruction of transcriptomes from RNA-seq data. Trinity combines three
diff --git a/debian/copyright b/debian/copyright
index 6633cf0..ee4832c 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,12 +1,18 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: trinityrnaseq
-Source: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.2.tar.gz
-Exclude: trinity_plugins/jellyfish-*.tar.gz
- util/support_scripts/ExitTester.jar
- Butterfly/src/lib/*.jar
+Source: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
+Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
+ util/support_scripts/ExitTester.jar
+ Butterfly/src/lib/*.jar
+ Butterfly/*.jar
+ Butterfly/prev_vers
+ trinity-plugins/rsem*.tar.gz
+ trinity-plugins/Trimmomatic*
Files: *
Copyright: © 2011 The Broad Institute, Inc; © 2014 trinityrnaseq
+Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
+Comment: trinity-plugins/GAL_0.2.1 is from http://www.sequenceontology.org/software/GAL_Code/
License: BSD-3-clause
All rights reserved.
.
@@ -35,8 +41,9 @@ License: BSD-3-clause
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Files: trinity-plugin/fastool*
+Files: trinity-plugin/*Fastool*
Copyright: (c) 2012 Francesco Strozzi
+Comment: https://github.com/fstrozzi/Fastool
License: Expat
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
@@ -58,3 +65,6 @@ License: Expat
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
+Files: debian/*
+Copyright: (c) 2015 Michael R. Crusoe, Michigan State University
+License: BSD-3-clause
diff --git a/debian/patches/chrysalis-makefile-auto b/debian/patches/chrysalis-makefile-auto
deleted file mode 100644
index e681069..0000000
--- a/debian/patches/chrysalis-makefile-auto
+++ /dev/null
@@ -1,212 +0,0 @@
-Description: <short summary of the patch>
- TODO: Put a short summary on the line above and replace this paragraph
- with a longer explanation of this change. Complete the meta-information
- with other relevant fields (see below for details). To make it easier, the
- information below has been extracted from the changelog. Adjust it or drop
- it.
- .
- trinityrnaseq (2.0.2-1) UNRELEASED; urgency=low
- .
- * Initial release (Closes: #<bug>)
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
---- /dev/null
-+++ trinityrnaseq-2.0.2/Chrysalis/Makefile_auto
-@@ -0,0 +1,184 @@
-+###
-+### This file is generated automatically. DO NOT MODIFY BY HAND!
-+###
-+
-+GraphFromFasta_MPI.o: $(SRC)/GraphFromFasta_MPI.cc $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/DeBruijnGraph.h $(SRC)/analysis/KmerTable.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/analysis/sequenceUtil.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+ReadsToTranscripts_MPI.o: $(SRC)/ReadsToTranscripts_MPI.cc $(SRC)/analysis/AACodons.h $(SRC)/analysis/CompMgr.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+ReadsToTranscripts_MPI_chang.o: $(SRC)/ReadsToTranscripts_MPI_chang.cc $(SRC)/analysis/AACodons.h $(SRC)/analysis/CompMgr.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+aligns/KmerAlignCore.o: $(SRC)/aligns/KmerAlignCore.cc $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h
-+analysis/AACodons.o: $(SRC)/analysis/AACodons.cc $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h
-+analysis/BreakTransByPairs.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/BreakTransByPairs.cc $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/Chrysalis.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/Chrysalis.cc $(SRC)/analysis/CompMgr.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/TranscriptomeGraph.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/CreateIwormFastaBundle.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/CreateIwormFastaBundle.cc $(SRC)/analysis/DNAVector.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/DNAVector.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.cc $(SRC)/analysis/DNAVector.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h
-+analysis/DeBruijnGraph.o: $(SRC)/analysis/DeBruijnGraph.cc $(SRC)/analysis/DeBruijnGraph.h $(SRC)/analysis/sequenceUtil.h $(SRC)/analysis/string_util.h
-+analysis/GraphFromFasta.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/DeBruijnGraph.h $(SRC)/analysis/GraphFromFasta.cc $(SRC)/analysis/KmerTable.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/analysis/sequenceUtil.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/IsoformAugment.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/IsoformAugment.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/JoinTransByPairs.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/JoinTransByPairs.cc $(SRC)/analysis/KmerTable.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/KmerTable.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.cc $(SRC)/analysis/KmerTable.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h
-+analysis/NonRedKmerTable.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/NonRedKmerTable.cc $(SRC)/analysis/NonRedKmerTable.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h
-+analysis/QuantifyGraph.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/CompMgr.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.h $(SRC)/analysis/QuantifyGraph.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/ReadsToTranscripts.o: $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/NonRedKmerTable.h $(SRC)/analysis/ReadsToTranscripts.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/RunButterfly.o: $(SRC)/analysis/RunButterfly.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/TranscriptomeFromVaryK.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/KmerTable.h $(SRC)/analysis/TranscriptomeFromVaryK.cc $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/TranscriptomeGraph.o: $(SRC)/aligns/KmerAlignCore.h $(SRC)/analysis/AACodons.h $(SRC)/analysis/DNAVector.h $(SRC)/analysis/TranscriptomeGraph.cc $(SRC)/analysis/TranscriptomeGraph.h $(SRC)/base/CommandLineParser.h $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/base/StringUtil.h $(SRC)/util/mutil.h
-+analysis/sequenceUtil.o: $(SRC)/analysis/sequenceUtil.cc $(SRC)/analysis/sequenceUtil.h $(SRC)/analysis/stacktrace.h
-+analysis/stacktrace.o: $(SRC)/analysis/stacktrace.cc $(SRC)/analysis/stacktrace.h
-+base/ErrorHandling.o: $(SRC)/base/ErrorHandling.cc $(SRC)/base/ErrorHandling.h
-+base/FileParser.o: $(SRC)/base/ErrorHandling.h $(SRC)/base/FileParser.cc $(SRC)/base/FileParser.h $(SRC)/base/SVector.h $(SRC)/util/mutil.h
-+base/StringUtil.o: $(SRC)/base/StringUtil.cc $(SRC)/base/StringUtil.h
-+util/mutil.o: $(SRC)/util/mutil.cc $(SRC)/util/mutil.h
-+BreakTransByPairs: checkLock
-+BreakTransByPairs: aligns/KmerAlignCore.o analysis/AACodons.o analysis/BreakTransByPairs.o analysis/DNAVector.o analysis/KmerTable.o analysis/NonRedKmerTable.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_BreakTransByPairs_temp.a
-+ $(AR) $(ARFLAGS) lib_BreakTransByPairs_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/BreakTransByPairs.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/BreakTransByPairs.o -L. $(LINK_LIBS) -l_BreakTransByPairs_temp
-+ /bin/rm lib_BreakTransByPairs_temp.a
-+Chrysalis: checkLock
-+Chrysalis: aligns/KmerAlignCore.o analysis/AACodons.o analysis/Chrysalis.o analysis/DNAVector.o analysis/TranscriptomeGraph.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_Chrysalis_temp.a
-+ $(AR) $(ARFLAGS) lib_Chrysalis_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/Chrysalis.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/TranscriptomeGraph.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/Chrysalis.o -L. $(LINK_LIBS) -l_Chrysalis_temp
-+ /bin/rm lib_Chrysalis_temp.a
-+CreateIwormFastaBundle: checkLock
-+CreateIwormFastaBundle: analysis/AACodons.o analysis/CreateIwormFastaBundle.o analysis/DNAVector.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_CreateIwormFastaBundle_temp.a
-+ $(AR) $(ARFLAGS) lib_CreateIwormFastaBundle_temp.a $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/CreateIwormFastaBundle.o $(OBJ)/analysis/DNAVector.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/CreateIwormFastaBundle.o -L. $(LINK_LIBS) -l_CreateIwormFastaBundle_temp
-+ /bin/rm lib_CreateIwormFastaBundle_temp.a
-+GraphFromFasta: checkLock
-+GraphFromFasta: aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/DeBruijnGraph.o analysis/GraphFromFasta.o analysis/KmerTable.o analysis/NonRedKmerTable.o analysis/sequenceUtil.o analysis/stacktrace.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_GraphFromFasta_temp.a
-+ $(AR) $(ARFLAGS) lib_GraphFromFasta_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/DeBruijnGraph.o $(OBJ)/analysis/GraphFromFasta.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/sequenceUtil.o $(OBJ)/analysis/stacktrace.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/GraphFromFasta.o -L. $(LINK_LIBS) -l_GraphFromFasta_temp
-+ /bin/rm lib_GraphFromFasta_temp.a
-+GraphFromFasta_MPI: checkLock
-+GraphFromFasta_MPI: GraphFromFasta_MPI.o aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/DeBruijnGraph.o analysis/KmerTable.o analysis/NonRedKmerTable.o analysis/sequenceUtil.o analysis/stacktrace.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_GraphFromFasta_MPI_temp.a
-+ $(AR) $(ARFLAGS) lib_GraphFromFasta_MPI_temp.a $(OBJ)/GraphFromFasta_MPI.o $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/DeBruijnGraph.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/sequenceUtil.o $(OBJ)/analysis/stacktrace.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/GraphFromFasta_MPI.o -L. $(LINK_LIBS) -l_GraphFromFasta_MPI_temp
-+ /bin/rm lib_GraphFromFasta_MPI_temp.a
-+IsoformAugment: checkLock
-+IsoformAugment: aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/IsoformAugment.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_IsoformAugment_temp.a
-+ $(AR) $(ARFLAGS) lib_IsoformAugment_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/IsoformAugment.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/IsoformAugment.o -L. $(LINK_LIBS) -l_IsoformAugment_temp
-+ /bin/rm lib_IsoformAugment_temp.a
-+JoinTransByPairs: checkLock
-+JoinTransByPairs: aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/JoinTransByPairs.o analysis/KmerTable.o analysis/NonRedKmerTable.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_JoinTransByPairs_temp.a
-+ $(AR) $(ARFLAGS) lib_JoinTransByPairs_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/JoinTransByPairs.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/JoinTransByPairs.o -L. $(LINK_LIBS) -l_JoinTransByPairs_temp
-+ /bin/rm lib_JoinTransByPairs_temp.a
-+QuantifyGraph: checkLock
-+QuantifyGraph: aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/KmerTable.o analysis/NonRedKmerTable.o analysis/QuantifyGraph.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_QuantifyGraph_temp.a
-+ $(AR) $(ARFLAGS) lib_QuantifyGraph_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/QuantifyGraph.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/QuantifyGraph.o -L. $(LINK_LIBS) -l_QuantifyGraph_temp
-+ /bin/rm lib_QuantifyGraph_temp.a
-+ReadsToTranscripts: checkLock
-+ReadsToTranscripts: analysis/AACodons.o analysis/DNAVector.o analysis/NonRedKmerTable.o analysis/ReadsToTranscripts.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_ReadsToTranscripts_temp.a
-+ $(AR) $(ARFLAGS) lib_ReadsToTranscripts_temp.a $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/ReadsToTranscripts.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/ReadsToTranscripts.o -L. $(LINK_LIBS) -l_ReadsToTranscripts_temp
-+ /bin/rm lib_ReadsToTranscripts_temp.a
-+ReadsToTranscripts_MPI: checkLock
-+ReadsToTranscripts_MPI: ReadsToTranscripts_MPI.o analysis/AACodons.o analysis/DNAVector.o analysis/NonRedKmerTable.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_ReadsToTranscripts_MPI_temp.a
-+ $(AR) $(ARFLAGS) lib_ReadsToTranscripts_MPI_temp.a $(OBJ)/ReadsToTranscripts_MPI.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/ReadsToTranscripts_MPI.o -L. $(LINK_LIBS) -l_ReadsToTranscripts_MPI_temp
-+ /bin/rm lib_ReadsToTranscripts_MPI_temp.a
-+ReadsToTranscripts_MPI_chang: checkLock
-+ReadsToTranscripts_MPI_chang: ReadsToTranscripts_MPI_chang.o analysis/AACodons.o analysis/DNAVector.o analysis/NonRedKmerTable.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_ReadsToTranscripts_MPI_chang_temp.a
-+ $(AR) $(ARFLAGS) lib_ReadsToTranscripts_MPI_chang_temp.a $(OBJ)/ReadsToTranscripts_MPI_chang.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/ReadsToTranscripts_MPI_chang.o -L. $(LINK_LIBS) -l_ReadsToTranscripts_MPI_chang_temp
-+ /bin/rm lib_ReadsToTranscripts_MPI_chang_temp.a
-+RunButterfly: checkLock
-+RunButterfly: analysis/RunButterfly.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_RunButterfly_temp.a
-+ $(AR) $(ARFLAGS) lib_RunButterfly_temp.a $(OBJ)/analysis/RunButterfly.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/RunButterfly.o -L. $(LINK_LIBS) -l_RunButterfly_temp
-+ /bin/rm lib_RunButterfly_temp.a
-+TranscriptomeFromVaryK: checkLock
-+TranscriptomeFromVaryK: aligns/KmerAlignCore.o analysis/AACodons.o analysis/DNAVector.o analysis/KmerTable.o analysis/NonRedKmerTable.o analysis/TranscriptomeFromVaryK.o base/ErrorHandling.o base/FileParser.o base/StringUtil.o util/mutil.o
-+ /bin/rm -f lib_TranscriptomeFromVaryK_temp.a
-+ $(AR) $(ARFLAGS) lib_TranscriptomeFromVaryK_temp.a $(OBJ)/aligns/KmerAlignCore.o $(OBJ)/analysis/AACodons.o $(OBJ)/analysis/DNAVector.o $(OBJ)/analysis/KmerTable.o $(OBJ)/analysis/NonRedKmerTable.o $(OBJ)/analysis/TranscriptomeFromVaryK.o $(OBJ)/base/ErrorHandling.o $(OBJ)/base/FileParser.o $(OBJ)/base/StringUtil.o $(OBJ)/util/mutil.o
-+ $(BIN)/checkLock $(BIN)/$@
-+ $(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ $(OBJ)/analysis/TranscriptomeFromVaryK.o -L. $(LINK_LIBS) -l_TranscriptomeFromVaryK_temp
-+ /bin/rm lib_TranscriptomeFromVaryK_temp.a
-+
-+# Target lists
-+
-+OBJECTS = \
-+ GraphFromFasta_MPI.o\
-+ ReadsToTranscripts_MPI.o\
-+ ReadsToTranscripts_MPI_chang.o\
-+ aligns/KmerAlignCore.o\
-+ analysis/AACodons.o\
-+ analysis/BreakTransByPairs.o\
-+ analysis/Chrysalis.o\
-+ analysis/CreateIwormFastaBundle.o\
-+ analysis/DNAVector.o\
-+ analysis/DeBruijnGraph.o\
-+ analysis/GraphFromFasta.o\
-+ analysis/IsoformAugment.o\
-+ analysis/JoinTransByPairs.o\
-+ analysis/KmerTable.o\
-+ analysis/NonRedKmerTable.o\
-+ analysis/QuantifyGraph.o\
-+ analysis/ReadsToTranscripts.o\
-+ analysis/RunButterfly.o\
-+ analysis/TranscriptomeFromVaryK.o\
-+ analysis/TranscriptomeGraph.o\
-+ analysis/sequenceUtil.o\
-+ analysis/stacktrace.o\
-+ base/ErrorHandling.o\
-+ base/FileParser.o\
-+ base/StringUtil.o\
-+ util/mutil.o\
-+
-+nolink: $(OBJECTS)
-+
-+EXECUTABLES = \
-+ BreakTransByPairs\
-+ Chrysalis\
-+ CreateIwormFastaBundle\
-+ GraphFromFasta\
-+ GraphFromFasta_MPI\
-+ IsoformAugment\
-+ JoinTransByPairs\
-+ QuantifyGraph\
-+ ReadsToTranscripts\
-+ ReadsToTranscripts_MPI\
-+ ReadsToTranscripts_MPI_chang\
-+ RunButterfly\
-+ TranscriptomeFromVaryK\
-+
-+everything: $(EXECUTABLES)
-+
-+.PHONY: analysis
-+analysis: \
-+ BreakTransByPairs\
-+ Chrysalis\
-+ CreateIwormFastaBundle\
-+ GraphFromFasta\
-+ IsoformAugment\
-+ JoinTransByPairs\
-+ QuantifyGraph\
-+ ReadsToTranscripts\
-+ RunButterfly\
-+ TranscriptomeFromVaryK\
-+
diff --git a/debian/patches/jellyfish-path b/debian/patches/jellyfish-path
index 1ac92ef..7e0d35e 100644
--- a/debian/patches/jellyfish-path
+++ b/debian/patches/jellyfish-path
@@ -1,7 +1,7 @@
Description:Jellyfish path
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -481,7 +481,7 @@
+@@ -36,7 +36,7 @@
my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
diff --git a/debian/patches/noExitTester b/debian/patches/noExitTester
index 6525074..084f783 100644
--- a/debian/patches/noExitTester
+++ b/debian/patches/noExitTester
@@ -1,7 +1,7 @@
Description:NoExitTester
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
-@@ -2072,32 +2072,6 @@
+@@ -2187,32 +2187,6 @@
die "Error, cannot find 'java'. Please be sure it is available within your \${PATH} setting and then try again.";
}
@@ -24,13 +24,13 @@ Description:NoExitTester
- };
-
- if ($@) {
-- print "-we properly captured the java failure status, as needed. Looking good.\n";
+- print "-we properly captured the java failure status, as needed. Looking good.\n" if $SEE;
- }
- else {
- print STDERR "-we are unable to properly capture java failure status. Please be sure that java (or any wrapper around java that's being used) can properly capture and propagate failure status before proceeding.\n";
- exit(1);
- }
-
- print "Java tests succeeded.\n";
- print "###################################\n\n";
+ print "Java tests succeeded.\n" if $SEE;
+ print "###################################\n\n" if $SEE;
diff --git a/debian/patches/series b/debian/patches/series
index 7bbb478..5cf7b6f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
chrysalis-make-tweak
noExitTester
-chrysalis-makefile-auto
jellyfish-path
diff --git a/debian/rules b/debian/rules
index adaa918..592e483 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,7 +16,7 @@ BUTTERFLY_LIBDIR := ${ROOT_DIR}/../Butterfly/src/lib
export CLASSPATH=/usr/share/java/collections15.jar:/usr/share/java/gnu-getopt.jar:${BUTTERFLY_LIBDIR}/jung-algorithms-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-api-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-api-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-graph-impl-2.0.1.jar
-SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/fastool trinity-plugins/parafly
+SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/parafly-code
BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq
@@ -53,3 +53,6 @@ override_dh_install:
${BASEDIR}/util/misc/capture_orig_n_unmapped_reads.pl \
${BASEDIR}/util/support_scripts/plugin_install_tests.sh \
${BASEDIR}/util/support_scripts/trinity_install_tests.sh
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git
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