Author: sascha-guest
Date: 2015-07-28 19:02:54 +0000 (Tue, 28 Jul 2015)
New Revision: 19729
Added:
trunk/packages/aegean/trunk/debian/README.source
trunk/packages/aegean/trunk/debian/man/canon-gff3.1
trunk/packages/aegean/trunk/debian/man/gaeval.1
trunk/packages/aegean/trunk/debian/man/pmrna.1
Modified:
trunk/packages/aegean/trunk/debian/aegean.docs
trunk/packages/aegean/trunk/debian/aegean.install
trunk/packages/aegean/trunk/debian/changelog
trunk/packages/aegean/trunk/debian/control
trunk/packages/aegean/trunk/debian/man/locuspocus.1
trunk/packages/aegean/trunk/debian/man/parseval.1
trunk/packages/aegean/trunk/debian/man/xtractore.1
trunk/packages/aegean/trunk/debian/patches/add_hardening
trunk/packages/aegean/trunk/debian/patches/add_version
trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs
trunk/packages/aegean/trunk/debian/patches/includepaths
Log:
update aegean to new upstream version
Added: trunk/packages/aegean/trunk/debian/README.source
===================================================================
--- trunk/packages/aegean/trunk/debian/README.source
(rev 0)
+++ trunk/packages/aegean/trunk/debian/README.source 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -0,0 +1 @@
+Please use the 'get-orig-source' rules target to get the source. It needs to
be repacked for dfsg reasons.
Modified: trunk/packages/aegean/trunk/debian/aegean.docs
===================================================================
--- trunk/packages/aegean/trunk/debian/aegean.docs 2015-07-28 18:05:22 UTC
(rev 19728)
+++ trunk/packages/aegean/trunk/debian/aegean.docs 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -1,3 +1,3 @@
README.md
VERSION
-CHANGELOG
+CHANGELOG.md
Modified: trunk/packages/aegean/trunk/debian/aegean.install
===================================================================
--- trunk/packages/aegean/trunk/debian/aegean.install 2015-07-28 18:05:22 UTC
(rev 19728)
+++ trunk/packages/aegean/trunk/debian/aegean.install 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -1,4 +1,7 @@
bin/parseval usr/bin
bin/locuspocus usr/bin
bin/xtractore usr/bin
+bin/canon-gff3 usr/bin
+bin/pmrna usr/bin
+bin/gaeval usr/bin
share/aegean usr/share
Modified: trunk/packages/aegean/trunk/debian/changelog
===================================================================
--- trunk/packages/aegean/trunk/debian/changelog 2015-07-28 18:05:22 UTC
(rev 19728)
+++ trunk/packages/aegean/trunk/debian/changelog 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -1,3 +1,9 @@
+aegean (0.13.0+dfsg-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <sas...@steinbiss.name> Tue, 28 Jul 2015 08:50:09 +0000
+
aegean (0.10.2+dfsg-1) unstable; urgency=low
* Initial release (Closes: #769162)
Modified: trunk/packages/aegean/trunk/debian/control
===================================================================
--- trunk/packages/aegean/trunk/debian/control 2015-07-28 18:05:22 UTC (rev
19728)
+++ trunk/packages/aegean/trunk/debian/control 2015-07-28 19:02:54 UTC (rev
19729)
@@ -5,7 +5,9 @@
Priority: optional
Build-Depends: debhelper (>= 9),
libcairo2-dev,
- libgenometools0-dev
+ libgenometools0-dev,
+ python,
+ git
Standards-Version: 3.9.6
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/aegean/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/aegean/trunk/
Added: trunk/packages/aegean/trunk/debian/man/canon-gff3.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/canon-gff3.1
(rev 0)
+++ trunk/packages/aegean/trunk/debian/man/canon-gff3.1 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH CANON-GFF3 "1" "July 2015" "canon-gff3 0.13" "User Commands"
+.SH NAME
+canon-gff3 \- create canonical GFF3
+.SH SYNOPSIS
+.B canon-gff3
+[\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 \/\fR...]
+.SH DESCRIPTION
+.IP
+Options:
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-i\fR|\-\-infer
+for transcript features lacking an explicitly
+declared gene feature as a parent, create this
+feature on\-they\-fly
+.TP
+\fB\-o\fR|\-\-outfile: STRING
+name of file to which GFF3 data will be
+written; default is terminal (stdout)
+.TP
+\fB\-s\fR|\-\-source: STRING
+reset the source of each feature to the given
+value
+.TP
+\fB\-v\fR|\-\-version
+print version number and exit
Added: trunk/packages/aegean/trunk/debian/man/gaeval.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/gaeval.1
(rev 0)
+++ trunk/packages/aegean/trunk/debian/man/gaeval.1 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -0,0 +1,42 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH GAEVAL "1" "July 2015" "gaeval 0.13" "User Commands"
+.SH NAME
+gaeval \- calculate coverage and intergrity scores for gene models based on
transcript alignments
+.SH SYNOPSIS
+.B gaeval
+[\fI\,options\/\fR] \fI\,alignments.gff3 genes.gff3 \/\fR[\fI\,moregenes.gff3
\/\fR...]
+.SH DESCRIPTION
+.IP
+Basic options:
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-v\fR|\-\-version
+print version number and exit
+.IP
+Weights for calculating integrity score (must add up to 1.0):
+.TP
+\fB\-a\fR|\-\-alpha: DOUBLE
+introns confirmed, or % expected CDS length for
+single\-exon genes; default is 0.6
+.TP
+\fB\-b\fR|\-\-beta: DOUBLE
+exon coverage; default is 0.3
+.TP
+\fB\-g\fR|\-\-gamma: DOUBLE
+% expected 5' UTR length; default is 0.05
+.TP
+\fB\-e\fR|\-\-epsilon: DOUBLE
+% expected 3' UTR length; default is 0.05
+.IP
+Expected feature lengths for calculating integrity score:
+.TP
+\fB\-c\fR|\-\-exp\-cds: INT
+expected CDS length (in bp); default is 400
+.TP
+\fB\-5\fR|\-\-exp\-5putr: INT
+expected 5' UTR length; default is 200
+.TP
+\fB\-3\fR|\-\-exp\-3putr: INT
+expected 3' UTR length; default is 100
Modified: trunk/packages/aegean/trunk/debian/man/locuspocus.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/locuspocus.1 2015-07-28 18:05:22 UTC
(rev 19728)
+++ trunk/packages/aegean/trunk/debian/man/locuspocus.1 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -1,12 +1,11 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.2.
-.TH LOCUSPOCUS "1" "November 2014" "locuspocus 10.2" "AEGeAn"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH LOCUSPOCUS "1" "July 2015" "locuspocus 0.13" "User Commands"
.SH NAME
locuspocus \- calculate locus coordinates for the given gene annotation
.SH SYNOPSIS
.B locuspocus
[\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 gff3file3 \/\fR...]
.SH DESCRIPTION
-LocusPocus: calculate locus coordinates for the given gene annotation
.IP
Basic options:
.TP
@@ -16,13 +15,12 @@
.TP
\fB\-h\fR|\-\-help
print this help message and exit
+.TP
+\fB\-v\fR|\-\-version
+print version number and exit
.IP
iLocus parsing:
.TP
-\fB\-i\fR|\-\-intloci
-parse and report interval loci rather than gene
-loci
-.TP
\fB\-l\fR|\-\-delta: INT
when parsing interval loci, use the following
delta to extend gene loci and include potential
@@ -33,8 +31,11 @@
iLoci at either end of the sequence
.TP
\fB\-e\fR|\-\-endsonly
-report only gene\-less iLoci at the ends of
-sequences (complement of \fB\-\-skipends\fR)
+report only empty iLoci at the ends of sequences
+(complement of \fB\-\-skipends\fR)
+.TP
+\fB\-y\fR|\-\-skipempty
+do not report empty iLoci
.IP
Output options:
.TP
@@ -59,7 +60,7 @@
print a mapping from each transcript annotation
to its corresponding locus to the given file
.TP
-\fB\-v\fR|\-\-verbose
+\fB\-V\fR|\-\-verbose
include all locus subfeatures (genes, RNAs, etc)
in the GFF3 output; default includes only locus
features
Modified: trunk/packages/aegean/trunk/debian/man/parseval.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/parseval.1 2015-07-28 18:05:22 UTC
(rev 19728)
+++ trunk/packages/aegean/trunk/debian/man/parseval.1 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -1,12 +1,11 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.2.
-.TH PARSEVAL "1" "November 2014" "parseval 10.2" "AEGeAn"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH PARSEVAL "1" "July 2015" "parseval 0.13" "User Commands"
.SH NAME
parseval \- comparative analysis of two alternative sources of annotation
.SH SYNOPSIS
.B parseval
[\fI\,options\/\fR] \fI\,reference.gff3 prediction.gff3\/\fR
.SH DESCRIPTION
-ParsEval: comparative analysis of two alternative sources of annotation
.IP
Basic options:
.TP
@@ -16,8 +15,15 @@
\fB\-h\fR|\-\-help:
Print help message and exit
.TP
-\fB\-v\fR|\-\-verbose:
+\fB\-l\fR|\-\-delta: INT
+Extend gene loci by this many nucleotides;
+default is 0
+.TP
+\fB\-V\fR|\-\-verbose:
Print verbose warning messages
+.TP
+\fB\-v\fR|\-\-version:
+Print version number and exit
.IP
Output options:
.TP
Added: trunk/packages/aegean/trunk/debian/man/pmrna.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/pmrna.1
(rev 0)
+++ trunk/packages/aegean/trunk/debian/man/pmrna.1 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH PMRNA "1" "July 2015" "pmrna 0.13" "User Commands"
+.SH NAME
+pmrna \- filter out all but the primary isoform from each gene of the input
+.SH SYNOPSIS
+.B pmrna
+[\fI\,options\/\fR] \fI\,< annot.gff3 > new.gff3\/\fR
+.SH DESCRIPTION
+.IP
+Options:
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-i\fR|\-\-introns
+flag indicating that introns are declared explicitly
+and do not need to be inferred from exon features;
+default is to infer introns
+.TP
+\fB\-l\fR|\-\-locus
+report a single representative mRNA for each locus
+instead of each gene
+.TP
+\fB\-m\fR|\-\-map: FILE
+write each gene/mRNA mapping to the specified file
+.TP
+\fB\-p\fR|\-\-pseudogenes
+disable pseudogene detection and correction
Modified: trunk/packages/aegean/trunk/debian/man/xtractore.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/xtractore.1 2015-07-28 18:05:22 UTC
(rev 19728)
+++ trunk/packages/aegean/trunk/debian/man/xtractore.1 2015-07-28 19:02:54 UTC
(rev 19729)
@@ -1,15 +1,12 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.2.
-.TH XTRACTORE "1" "November 2014" "xtractore 10.2" "AEGeAn"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH XTRACTORE "1" "July 2015" "xtractore 0.13" "User Commands"
.SH NAME
xtractore \- extract sequences corresponding to annotated features from the
given sequence file
.SH SYNOPSIS
.B xtractore
[\fI\,options\/\fR] \fI\,features.gff3 sequences.fasta\/\fR
.SH DESCRIPTION
-xtractore: extract sequences corresponding to annotated features from the
.IP
-given sequence file
-.IP
Options:
.TP
\fB\-h\fR|\-\-help
@@ -28,7 +25,10 @@
feature type to extract; can be used multiple
times to extract features of multiple types
.TP
-\fB\-v\fR|\-\-verbose
+\fB\-v\fR|\-\-version
+print version number and exit
+.TP
+\fB\-V\fR|\-\-verbose
print verbose warning and error messages
.TP
\fB\-w\fR|\-\-width: INT
Modified: trunk/packages/aegean/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/add_hardening 2015-07-28
18:05:22 UTC (rev 19728)
+++ trunk/packages/aegean/trunk/debian/patches/add_hardening 2015-07-28
19:02:54 UTC (rev 19729)
@@ -1,12 +1,12 @@
Description: Add_hardening
--- a/Makefile
+++ b/Makefile
-@@ -55,7 +55,7 @@
+@@ -48,7 +48,7 @@
ifneq ($(debug),no)
CFLAGS += -g
endif
-LDFLAGS=-lgenometools -lm \
+LDFLAGS+=-lgenometools -lm \
- -L$(prefix)/lib
+ -L$(prefix)/lib \
+ -L/usr/local/lib
ifdef lib
- LDFLAGS += -L$(lib)
Modified: trunk/packages/aegean/trunk/debian/patches/add_version
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/add_version 2015-07-28
18:05:22 UTC (rev 19728)
+++ trunk/packages/aegean/trunk/debian/patches/add_version 2015-07-28
19:02:54 UTC (rev 19729)
@@ -1,56 +1,60 @@
Description: Add_version
---- /dev/null
-+++ b/VERSION
-@@ -0,0 +1 @@
-+0.10.2
--- a/Makefile
+++ b/Makefile
-@@ -95,39 +95,39 @@
-
+@@ -95,47 +95,47 @@
$(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
@- mkdir -p obj
-- $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
+ @ echo "[compile $*]"
+- @ $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
- $(VN_OBJS): obj/%.o : src/VAnG/%.c inc/VAnG/%.h inc/core/AgnVersion.h
- @- mkdir -p obj
-- $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
-
$(PE_EXE): src/ParsEval/parseval.c src/ParsEval/pe_options.c
src/ParsEval/pe_utils.c src/ParsEval/pe_options.h src/ParsEval/pe_utils.h
$(AGN_OBJS)
- @- mkdir -p bin
-- $(CC) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS)
src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c
$(LDFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@
$(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c
src/ParsEval/pe_utils.c $(LDFLAGS)
+ @ mkdir -p bin
+ @ echo "[compile ParsEval]"
+- @ $(CC) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS)
src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@
$(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c
src/ParsEval/pe_utils.c $(LDFLAGS)
$(CN_EXE): src/canon-gff3.c $(AGN_OBJS)
- @- mkdir -p bin
-- $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c
$(LDFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/canon-gff3.c $(LDFLAGS)
-
- $(VN_EXE): src/VAnG/vang.c $(VN_OBJS)
- @- mkdir -p bin
-- $(CC) $(CFLAGS) $(INCS) -o $@ $(VN_OBJS) src/VAnG/vang.c
$(LDFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(VN_OBJS)
src/VAnG/vang.c $(LDFLAGS)
+ @ mkdir -p bin
+ @ echo "[compile CanonGFF3]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/canon-gff3.c $(LDFLAGS)
$(LP_EXE): src/locuspocus.c $(AGN_OBJS)
- @- mkdir -p bin
-- $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c
$(LDFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/locuspocus.c $(LDFLAGS)
+ @ mkdir -p bin
+ @ echo "[compile LocusPocus]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/locuspocus.c $(LDFLAGS)
+ $(GV_EXE): src/gaeval.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile GAEVAL]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/gaeval.c $(LDFLAGS)
+
$(XT_EXE): src/xtractore.c $(AGN_OBJS)
- @- mkdir -p bin
-- $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c
$(LDFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/xtractore.c $(LDFLAGS)
+ @ mkdir -p bin
+ @ echo "[compile Xtractore]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/xtractore.c $(LDFLAGS)
$(RP_EXE): src/pmrna.c $(AGN_OBJS)
- @- mkdir -p bin
-- $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/pmrna.c $(LDFLAGS)
+ @ mkdir -p bin
+ @ echo "[compile $@]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/pmrna.c $(LDFLAGS)
+ $(TD_EXE): src/tidygff3.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile $@]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/tidygff3.c $(LDFLAGS)
+
$(UT_EXE): test/unittests.c $(AGN_OBJS)
- @- mkdir -p bin
-- $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c
$(LDFLAGS)
-+ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
test/unittests.c $(LDFLAGS)
+ @ mkdir -p bin
+ @ echo "[compile unit tests]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c
$(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
test/unittests.c $(LDFLAGS)
libaegean.a: $(AGN_OBJS)
- ar ru libaegean.a $(AGN_OBJS)
+ @ echo "[create libaegean]"
Modified: trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs
2015-07-28 18:05:22 UTC (rev 19728)
+++ trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs
2015-07-28 19:02:54 UTC (rev 19729)
@@ -1,7 +1,7 @@
Description: Fix_m64_on_some_archs
--- a/Makefile
+++ b/Makefile
-@@ -37,6 +37,8 @@
+@@ -29,6 +29,8 @@
CC=gcc
CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
GTFLAGS=prefix=$(prefix)
@@ -10,7 +10,7 @@
ifeq ($(cairo),no)
CFLAGS += -DWITHOUT_CAIRO
GTFLAGS += cairo=no
-@@ -48,8 +50,10 @@
+@@ -40,8 +42,10 @@
CFLAGS += -O3
endif
ifneq ($(64bit),no)
@@ -23,7 +23,7 @@
endif
ifneq ($(debug),no)
CFLAGS += -g
-@@ -72,7 +76,7 @@
+@@ -66,7 +70,7 @@
# Targets
all: $(BINS) libaegean.a
@@ -31,50 +31,13 @@
+
install: all
- @- test -d $(prefix)/bin || mkdir -p $(prefix)/bin
-@@ -86,11 +90,11 @@
- @- test -d $(prefix)/share/aegean || mkdir -p
$(prefix)/share/aegean
- cp -r data/share/* $(prefix)/share/aegean/
+ @ mkdir -p $(prefix)/bin/
+@@ -142,7 +146,7 @@
+ @ ar ru libaegean.a $(AGN_OBJS)
--uninstall:
-+uninstall:
- rm -r $(prefix)/$(PE_EXE)
- rm -r $(prefix)/share/parseval
+ inc/core/AgnVersion.h:
+- @- echo "[print $@]"
++ @ echo "[print $@]"
+ @ data/scripts/version.py > $@
--clean:
-+clean:
- rm -rf README $(BINS) $(UT_EXE) libaegean.a $(CLSS_MDL_OBJS)
inc/core/AgnVersion.h bin/*.dSYM
-
- $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
-@@ -100,7 +104,7 @@
- $(VN_OBJS): obj/%.o : src/VAnG/%.c inc/VAnG/%.h inc/core/AgnVersion.h
- @- mkdir -p obj
- $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
--
-+
- $(PE_EXE): src/ParsEval/parseval.c src/ParsEval/pe_options.c
src/ParsEval/pe_utils.c src/ParsEval/pe_options.h src/ParsEval/pe_utils.h
$(AGN_OBJS)
- @- mkdir -p bin
- $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@
$(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c
src/ParsEval/pe_utils.c $(LDFLAGS)
-@@ -108,7 +112,7 @@
- $(CN_EXE): src/canon-gff3.c $(AGN_OBJS)
- @- mkdir -p bin
- $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS)
src/canon-gff3.c $(LDFLAGS)
--
-+
- $(VN_EXE): src/VAnG/vang.c $(VN_OBJS)
- @- mkdir -p bin
- $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(VN_OBJS)
src/VAnG/vang.c $(LDFLAGS)
-@@ -132,11 +136,11 @@
- libaegean.a: $(AGN_OBJS)
- ar ru libaegean.a $(AGN_OBJS)
-
--inc/core/AgnVersion.h:
-+inc/core/AgnVersion.h:
- @- bash -c "if [ -d .git ]; then perl
data/scripts/version.pl > inc/core/AgnVersion.h; else perl
data/scripts/version.pl --link=$(AGN_LINK) --date=$(AGN_DATE)
--version=$(AGN_VERSION) > inc/core/AgnVersion.h; fi"
-
test: agn-test
--
-+
-
- agn-test: all
- @ $(LDPATH) $(MEMCHECK) bin/unittests
Modified: trunk/packages/aegean/trunk/debian/patches/includepaths
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/includepaths 2015-07-28
18:05:22 UTC (rev 19728)
+++ trunk/packages/aegean/trunk/debian/patches/includepaths 2015-07-28
19:02:54 UTC (rev 19729)
@@ -1,16 +1,17 @@
Description: Includepaths
--- a/Makefile
+++ b/Makefile
-@@ -1,7 +1,6 @@
+@@ -1,8 +1,6 @@
#---Begin configuration---#
#---Begin configuration---#
-prefix=/usr/local
- AGN_LINK=https://github.com/standage/AEGeAn
- AGN_DATE=2014
- AGN_VERSION=0.10.1
-@@ -36,7 +35,7 @@
+-
+ #----End configuration----#
+ #----End configuration----#
+@@ -29,7 +27,7 @@
+
# Compilation settings
CC=gcc
-CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
@@ -18,45 +19,20 @@
GTFLAGS=prefix=$(prefix)
ifeq ($(cairo),no)
CFLAGS += -DWITHOUT_CAIRO
-@@ -60,7 +59,7 @@
- ifdef lib
- LDFLAGS += -L$(lib)
- endif
--INCS=-I src/genometools/src -I src/genometools/obj -I
/usr/local/include/genometools \
-+INCS=-I src/genometools/src -I src/genometools/obj -I
/usr/include/genometools \
- -I inc/core -I inc/ParsEval -I inc/VAnG \
- -I /usr/include/cairo -I /sw/include/cairo
+@@ -57,6 +55,7 @@
+ INCS=$(shell pkg-config --silence-errors --cflags-only-I cairo) \
+ -I inc/core \
+ -I /usr/local/include/genometools \
++ -I /usr/include/genometools \
+ -I $(prefix)/include/genometools
ifeq ($(memcheck),yes)
-@@ -76,22 +75,23 @@
-
+ MEMCHECK=valgrind --leak-check=full --show-reachable=yes --error-exitcode=1
\
+@@ -91,7 +90,7 @@
+ rm $(prefix)/lib/libaegean.a
- install: all
-- @- test -d $(prefix)/bin || mkdir $(prefix)/bin
-- cp $(PE_EXE) $(XT_EXE) $(LP_EXE) $(prefix)/bin/.
-- cp libaegean.a $(prefix)/lib/.
-- @- test -d $(prefix)/include/aegean || mkdir
$(prefix)/include/aegean
-+ @- test -d $(prefix)/bin || mkdir -p $(prefix)/bin
-+ cp $(PE_EXE) $(XT_EXE) $(LP_EXE) $(prefix)/bin/
-+ @- test -d $(prefix)/lib || mkdir -p $(prefix)/lib
-+ cp libaegean.a $(prefix)/lib/
-+ @- test -d $(prefix)/include/aegean || mkdir -p
$(prefix)/include/aegean
- @- rm -f $(prefix)/include/aegean/*
-- cp inc/core/*.h $(prefix)/include/aegean/.
-- @- test -d $(prefix)/share || mkdir $(prefix)/share
-- @- test -d $(prefix)/share/aegean || mkdir
$(prefix)/share/aegean
-- cp -r data/share/* $(prefix)/share/aegean/.
-+ cp inc/core/*.h $(prefix)/include/aegean/
-+ @- test -d $(prefix)/share || mkdir -p $(prefix)/share
-+ @- test -d $(prefix)/share/aegean || mkdir -p
$(prefix)/share/aegean
-+ cp -r data/share/* $(prefix)/share/aegean/
-
- uninstall:
- rm -r $(prefix)/$(PE_EXE)
- rm -r $(prefix)/share/parseval
-
clean:
-- rm -rf $(BINS) $(UT_EXE) libaegean.a $(CLSS_MDL_OBJS)
inc/core/AgnVersion.h bin/*.dSYM
-+ rm -rf README $(BINS) $(UT_EXE) libaegean.a $(CLSS_MDL_OBJS)
inc/core/AgnVersion.h bin/*.dSYM
+- rm -rf $(BINS) libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h
bin/*.dSYM
++ rm -rf README $(BINS) libaegean.a $(AGN_OBJS)
inc/core/AgnVersion.h bin/*.dSYM
$(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
@- mkdir -p obj
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