[med-svn] r5758 - in trunk/packages/vienna-rna/trunk/debian: . patches
Alexandre Mestiashvili
malex-guest at alioth.debian.org
Sat Jan 29 19:06:48 UTC 2011
Author: malex-guest
Date: 2011-01-29 19:06:43 +0000 (Sat, 29 Jan 2011)
New Revision: 5758
Modified:
trunk/packages/vienna-rna/trunk/debian/patches/readseq-exclude.patch
trunk/packages/vienna-rna/trunk/debian/rules
trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
Log:
manpage one more time
Modified: trunk/packages/vienna-rna/trunk/debian/patches/readseq-exclude.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/readseq-exclude.patch 2011-01-29 18:53:10 UTC (rev 5757)
+++ trunk/packages/vienna-rna/trunk/debian/patches/readseq-exclude.patch 2011-01-29 19:06:43 UTC (rev 5758)
@@ -1,8 +1,8 @@
Readseq is a different packages which a standalone package. So we don't need to build it as a part of vienna-rna.
-Index: vienna-rna-1.8.4/Makefile.in
+Index: viennarna-1.8.4/Makefile.in
===================================================================
---- vienna-rna-1.8.4.orig/Makefile.in 2011-01-29 12:17:01.000000000 +0100
-+++ vienna-rna-1.8.4/Makefile.in 2011-01-29 12:17:11.000000000 +0100
+--- viennarna-1.8.4.orig/Makefile.in 2009-10-13 13:44:34.000000000 +0200
++++ viennarna-1.8.4/Makefile.in 2011-01-29 19:56:32.000000000 +0100
@@ -234,7 +234,7 @@
#DIST_SUBDIRS = lib Progs man Utils AliFold H Perl Cluster
@@ -12,3 +12,180 @@
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-recursive
+Index: viennarna-1.8.4/man/RNALfold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNALfold.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNALfold.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNALFOLD" "l" "1.5" "Ivo Hofacker" "ViennaRNA"
++.TH "RNALFOLD" "1" "1.5" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNALfold \- calculate locally stable secondary structures of RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAaliduplex.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAaliduplex.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAaliduplex.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,4 +1,4 @@
+-.TH "RNAaliduplex" "l" "0.0.1" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAaliduplex" "1" "0.0.1" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ .LP
+ RNAaliduplex \- Predict conserved RNA-RNA interactions between two alignments
+Index: viennarna-1.8.4/man/RNAalifold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAalifold.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAalifold.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,6 +1,6 @@
+ .\" -*-nroff-*-
+ .\" .ER
+-.TH "RNAalifold" "l" "1.8" "Ivo Hofacker" "ViennaRNA"
++.TH "RNAalifold" "1" "1.8" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAalifold \- calculate secondary structures for a set of aligned RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAcofold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAcofold.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAcofold.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNACOFOLD" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
++.TH "RNACOFOLD" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAcofold \- calculate secondary structures of two RNAs with dimerization
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAdistance.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAdistance.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAdistance.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNADISTANCE" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNADISTANCE" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAdistance \- calculate distances between RNA secondary structures
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAduplex.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAduplex.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAduplex.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,4 +1,4 @@
+-.TH "RNAduplex" "l" "0.0.1" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAduplex" "1" "0.0.1" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ .LP
+ RNAduplex \- Compute the structure upon hybridization of two RNA strands
+Index: viennarna-1.8.4/man/RNAeval.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAeval.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAeval.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAEVAL" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAEVAL" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAEVAL \- calculate energy of RNA sequences on given secondary structure
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAfold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAfold.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAfold.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,6 +1,6 @@
+ .\" -*-nroff-*-
+ .\" .ER
+-.TH "RNAFOLD" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
++.TH "RNAFOLD" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAfold \- calculate secondary structures of RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAheat.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAheat.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAheat.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAHEAT" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAHEAT" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAheat \- calculate specific heat of RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAinverse.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAinverse.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAinverse.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAINVERSE" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAINVERSE" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAINVERSE \- find RNA sequences with given secondary structure
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNApaln.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNApaln.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNApaln.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAPDIST" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNApaln \- RNA alignment based on sequence base pairing propensities
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNApdist.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNApdist.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNApdist.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAPDIST" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNApdist \- calculate distances between thermodynamic RNA secondary
+ structures ensembles
+Index: viennarna-1.8.4/man/RNAplfold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAplfold.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAplfold.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPLFOLD" "l" "1.8" "Stephan Bernhart" "ViennaRNA"
++.TH "RNAPLFOLD" "1" "1.8" "Stephan Bernhart" "ViennaRNA"
+ .SH "NAME"
+ RNAplfold \- calculate locally stable secondary structure - pair probabilities
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAplot.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAplot.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAplot.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPLOT" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAPLOT" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAplot \- Draw RNA Secondary Structures
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAsubopt.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAsubopt.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAsubopt.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,6 +1,6 @@
+ \" -*-nroff-*-
+ .\" .ER
+-.TH "RNASUBOPT" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNASUBOPT" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAsubopt \- calculate suboptimal secondary structures of RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAup.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAup.1.in 2011-01-29 20:01:09.000000000 +0100
++++ viennarna-1.8.4/man/RNAup.1.in 2011-01-29 20:01:15.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAUP" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
++.TH "RNAUP" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAup \- calculates the thermodynamics of RNA-RNA interactions
+ .SH "SYNOPSIS"
Modified: trunk/packages/vienna-rna/trunk/debian/rules
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/rules 2011-01-29 18:53:10 UTC (rev 5757)
+++ trunk/packages/vienna-rna/trunk/debian/rules 2011-01-29 19:06:43 UTC (rev 5758)
@@ -59,6 +59,7 @@
#$(MAKE) doc
touch $@
+ dh_quilt_patch
clean:
dh_testdir
dh_testroot
@@ -77,7 +78,6 @@
install: install-indep install-arch
install-indep:
- dh_quilt_patch
dh_testdir
dh_testroot
dh_clean -k -i --exclude ./Readseq/ureadseq.c.orig --exclude ./Readseq/readseq.c.orig --exclude ./Readseq/ureadseq.h.orig
@@ -90,7 +90,6 @@
dh_install -i
install-arch:
- dh_quilt_patch
dh_testdir
dh_testroot
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.install 2011-01-29 18:53:10 UTC (rev 5757)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.install 2011-01-29 19:06:43 UTC (rev 5758)
@@ -17,8 +17,8 @@
Progs/RNAcofold /usr/bin
Progs/RNAduplex /usr/bin
#Utils/Fold /usr/bin moved to examples
-#Utils/b2ct /usr/bin
-#Utils/popt /usr/bin
+Utils/b2ct /usr/bin
+Utils/popt /usr/bin
#Utils/ct2b /usr/bin
#Utils/b2mt /usr/bin
#Utils/coloraln /usr/bin
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