[med-svn] r45 - in trunk/packages/probcons/trunk: . debian
debian/patches
Charles Plessy
charles-guest at costa.debian.org
Sun Jun 4 15:13:28 UTC 2006
Author: charles-guest
Date: 2006-06-04 15:13:27 +0000 (Sun, 04 Jun 2006)
New Revision: 45
Added:
trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch
trunk/packages/probcons/trunk/debian/probcons-extra.dirs
trunk/packages/probcons/trunk/debian/probcons-extra.install
trunk/packages/probcons/trunk/debian/probcons-extra.manpages
trunk/packages/probcons/trunk/debian/probcons.copyright
trunk/packages/probcons/trunk/debian/probcons.dirs
trunk/packages/probcons/trunk/debian/probcons.docs
trunk/packages/probcons/trunk/debian/probcons.install
trunk/packages/probcons/trunk/debian/probcons.manpages
Removed:
trunk/packages/probcons/trunk/debian/copyright
trunk/packages/probcons/trunk/debian/dirs
trunk/packages/probcons/trunk/debian/docs
trunk/packages/probcons/trunk/debian/install
trunk/packages/probcons/trunk/debian/manpages
trunk/packages/probcons/trunk/debian/patches/11-Renames-compare-in-Makefile.dpatch
Modified:
trunk/packages/probcons/trunk/Makefile
trunk/packages/probcons/trunk/debian/README.Debian
trunk/packages/probcons/trunk/debian/control
trunk/packages/probcons/trunk/debian/patches/00list
trunk/packages/probcons/trunk/debian/pc-compare.1.xml
trunk/packages/probcons/trunk/debian/probcons-RNA.1
trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml
trunk/packages/probcons/trunk/debian/probcons.1.xml
trunk/packages/probcons/trunk/debian/rules
Log:
Splitting into probcons and probcons-extra.
Modified: trunk/packages/probcons/trunk/Makefile
===================================================================
--- trunk/packages/probcons/trunk/Makefile 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/Makefile 2006-06-04 15:13:27 UTC (rev 45)
@@ -16,6 +16,7 @@
################################################################################
OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
+OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.10"
# debug mode
#CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
@@ -25,13 +26,16 @@
# release mode
#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
+
CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
+
################################################################################
# 3) Dependencies
################################################################################
-TARGETS = probcons compare project makegnuplot
+TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot
.PHONY : all
all : $(TARGETS)
@@ -39,17 +43,20 @@
probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
$(CXX) $(CXXFLAGS) -lm -o probcons Main.cc
-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
+pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+ $(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
+probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
+ $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
+
fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
- $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
+pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+ $(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
-makegnuplot : MakeGnuPlot.cc
- $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
+pc-makegnuplot : MakeGnuPlot.cc
+ $(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
.PHONY : clean
clean:
Modified: trunk/packages/probcons/trunk/debian/README.Debian
===================================================================
--- trunk/packages/probcons/trunk/debian/README.Debian 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/README.Debian 2006-06-04 15:13:27 UTC (rev 45)
@@ -1,8 +1,9 @@
probcons for Debian
-------------------
-* The "compare" program has been renamed "pc-compare" because there is already
- a "compare" program in another Debian package.
+* The "compare", "project" and "makegnuplot" programs are located in the
+ probcons-extra package and renamed "pc-compare", "pc-project" and
+ "pc-makegnuplot" to avoid collision with other program names.
* This package contains an additionnal binary which is not in the original
distribution of ProbCons: probcons-RNA. It is an experimental version of
Modified: trunk/packages/probcons/trunk/debian/control
===================================================================
--- trunk/packages/probcons/trunk/debian/control 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/control 2006-06-04 15:13:27 UTC (rev 45)
@@ -2,24 +2,39 @@
Section: science
Priority: optional
Maintainer: Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 4.0.0), xsltproc, docbook-xml, docbook-xsl, sharutils
+Build-Depends: debhelper (>= 4.0.0), xsltproc, docbook-xml, docbook-xsl
Standards-Version: 3.7.2
Package: probcons
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: gnuplot-nox | gnuplot-x11
+Suggests: probcons-extra
Description: PROBabilistic CONSistency-based multiple sequence alignment
- PROBCONS is a tool for generating multiple alignments of protein
- sequences. Using a combination of probabilistic modeling and
- consistency-based alignment techniques, PROBCONS has achieved the
- highest accuracies of all alignment methods to date. On the BAliBASE
- benchmark alignment database, alignments produced by PROBCONS show
- statistically significant improvement over current programs, containing
- an average of 7% more correctly aligned columns than those of T-Coffee,
- 11% more correctly aligned columns than those of CLUSTAL W, and 14%
- more correctly aligned columns than those of DIALIGN. Probcons is
- published in Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and
- Batzoglou, S. 2005. Genome Research 15: 330-340.
+ Tool for generating multiple alignments of protein sequences. Using a
+ combination of probabilistic modeling and consistency-based alignment
+ techniques, PROBCONS has achieved the highest accuracies of all alignment
+ methods to date. On the BAliBASE benchmark alignment database, alignments
+ produced by PROBCONS show statistically significant improvement over current
+ programs, containing an average of 7% more correctly aligned columns than
+ those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W,
+ and 14% more correctly aligned columns than those of DIALIGN. Probcons is
+ published in Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
+ 2005. Genome Research 15: 330-340.
.
Homepage: http://probcons.stanford.edu/
+
+Package: probcons-extra
+Architecture: any
+Depends: probcons, ${shlibs:Depends}, ${misc:Depends}
+Suggests: gnuplot-nox | gnuplot-x11
+Description: Extra programs from the probcons package
+ Contains the convert, project and makgnuplot programs from the probcons
+ package, which have been renamed to pc-compare, pc-project and pc-makegnuplot
+ respectively to avoid collisions with other program names. These programs are
+ mostly useful for testing purposes and are not required for the normal usage of
+ Probcons.
+ .
+ Probcons is a tool for generating multiple alignments of protein
+ sequences.
+ .
+ Homepage: http://probcons.stanford.edu/
Deleted: trunk/packages/probcons/trunk/debian/copyright
===================================================================
--- trunk/packages/probcons/trunk/debian/copyright 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/copyright 2006-06-04 15:13:27 UTC (rev 45)
@@ -1,13 +0,0 @@
-This package was debianized by Charles Plessy
-<charles-debian-nospam at plessy.org> on Wed, 3 May 2006. The packaging and the
-manpages work are in the public domain unless stated otherwise.
-
-ProbCons was downloaded from http://probcons.stanford.edu/probcons_v1_10.tar.gz
-The modified files for RNA alignment were downloaded from http://probcons.stanford.edu/probconsRNA.tar.gz
-The ProbCons manual was downloaded from http://probcons.stanford.edu/manual.pdf
-
-This software is in the public domain.
-
-ProbCons was written by by Chuong Do <chuongdo at cs.stanford.edu> in
-collaboration with Michael Brudno in the research group of Serafim Batzoglou,
-Department of Computer Science, Stanford University.
Deleted: trunk/packages/probcons/trunk/debian/dirs
===================================================================
--- trunk/packages/probcons/trunk/debian/dirs 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/dirs 2006-06-04 15:13:27 UTC (rev 45)
@@ -1 +0,0 @@
-usr/bin
Deleted: trunk/packages/probcons/trunk/debian/docs
===================================================================
--- trunk/packages/probcons/trunk/debian/docs 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/docs 2006-06-04 15:13:27 UTC (rev 45)
@@ -1,2 +0,0 @@
-README
-manual.pdf
Deleted: trunk/packages/probcons/trunk/debian/install
===================================================================
--- trunk/packages/probcons/trunk/debian/install 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/install 2006-06-04 15:13:27 UTC (rev 45)
@@ -1,6 +0,0 @@
-probcons usr/bin/
-probcons-RNA usr/bin/
-project usr/bin/
-makegnuplot usr/bin/
-pc-compare usr/bin/
-
Deleted: trunk/packages/probcons/trunk/debian/manpages
===================================================================
--- trunk/packages/probcons/trunk/debian/manpages 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/manpages 2006-06-04 15:13:27 UTC (rev 45)
@@ -1,5 +0,0 @@
-debian/makegnuplot.1
-debian/pc-compare.1
-debian/probcons.1
-debian/probcons-RNA.1
-debian/project.1
Modified: trunk/packages/probcons/trunk/debian/patches/00list
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/00list 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/patches/00list 2006-06-04 15:13:27 UTC (rev 45)
@@ -1,2 +1,2 @@
10_add-RNA-in-Makefile.dpatch
-11-Renames-compare-in-Makefile.dpatch
+11-Rename-programs-in-Makefile.dpatch
Added: trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,47 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 11-Rename-programs-in-Makefile.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+## This patch is hereby released in the public domain.
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Renames compare, project and makegnuplot to pc-compare, pc-project and
+## DP: pc-makegnuplot
+
+ at DPATCH@
+
+--- probcons-1.10-orig/Makefile 2006-06-04 22:01:10.000000000 +0900
++++ probcons-1.10/Makefile 2006-06-04 21:53:30.000000000 +0900
+@@ -35,7 +35,7 @@
+ # 3) Dependencies
+ ################################################################################
+
+-TARGETS = probcons probcons-RNA compare project makegnuplot
++TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot
+
+ .PHONY : all
+ all : $(TARGETS)
+@@ -43,8 +43,8 @@
+ probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
+ $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc
+
+-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
++pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
++ $(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
+
+ probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
+ $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
+@@ -52,11 +52,11 @@
+ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
+ $(CXX) $(CXXFLAGS) -o fixref FixRef.cc
+
+-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+- $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
++pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
++ $(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
+
+-makegnuplot : MakeGnuPlot.cc
+- $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
++pc-makegnuplot : MakeGnuPlot.cc
++ $(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
+
+ .PHONY : clean
+ clean:
Property changes on: trunk/packages/probcons/trunk/debian/patches/11-Rename-programs-in-Makefile.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/probcons/trunk/debian/patches/11-Renames-compare-in-Makefile.dpatch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/11-Renames-compare-in-Makefile.dpatch 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/patches/11-Renames-compare-in-Makefile.dpatch 2006-06-04 15:13:27 UTC (rev 45)
@@ -1,31 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 11-Renames-compare-in-Makefile.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
-## This patch is hereby released in the public domain.
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Renames compare to pc-compare
-
- at DPATCH@
-
---- probcons-1.10/Makefile 2006-05-07 13:52:26.000000000 +0900
-+++ probcons-1.10.modified/Makefile 2006-05-07 13:53:04.000000000 +0900
-@@ -35,7 +35,7 @@
- # 3) Dependencies
- ################################################################################
-
--TARGETS = probcons probcons-RNA compare project makegnuplot
-+TARGETS = probcons probcons-RNA pc-compare project makegnuplot
-
- .PHONY : all
- all : $(TARGETS)
-@@ -43,8 +43,8 @@
- probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
- $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc
-
--compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
-- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
-+pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
-+ $(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
-
- probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
- $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
Modified: trunk/packages/probcons/trunk/debian/pc-compare.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/pc-compare.1.xml 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/pc-compare.1.xml 2006-06-04 15:13:27 UTC (rev 45)
@@ -8,7 +8,7 @@
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
<!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>PROBCONS</refentrytitle>">
+ <!ENTITY dhucpackage "<refentrytitle>PROBCONS-EXTRA</refentrytitle>">
<!ENTITY dhpackage "pc-compare">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
@@ -56,9 +56,14 @@
</arg>
</cmdsynopsis>
</refsynopsisdiv>
+ <refsect1>
+ <title>NOTE</title>
+ <para>&dhpackage; is named <filename>compare</filename> in the original sources, but has been remamed to avoid collision with other program names.</para>
+ </refsect1>
+
<refsect1>
<title>SEE ALSO</title>
- <para>makegnufile (1), project (1), probcons (1), which are distributed together with probcons.</para>
+ <para>pc-makegnuplot (1) and pc-project (1), from the probcons-extra package, and probcons (1) and probcons-RNA (1) from the probcons package.</para>
</refsect1>
<refsect1>
@@ -69,7 +74,7 @@
<refsect1>
<title>AUTHORS</title>
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email>in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
+ <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
<para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
</para>
Modified: trunk/packages/probcons/trunk/debian/probcons-RNA.1
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-RNA.1 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons-RNA.1 2006-06-04 15:13:27 UTC (rev 45)
@@ -28,7 +28,7 @@
.SH "AUTHORS"
.PP
-probcons\-RNA was written by Chuong Do <chuongdo at cs\&.stanford\&.edu>in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\&.
+probcons\-RNA was written by Chuong Do <chuongdo at cs\&.stanford\&.edu> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\&.
.PP
This manual page was written by Charles Plessy <charles\-debian\-nospam at plessy\&.org> for the Debian™ system (but may be used by others)\&.
Modified: trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml 2006-06-04 15:13:27 UTC (rev 45)
@@ -48,7 +48,7 @@
<refsect1>
<title>AUTHORS</title>
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email>in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
+ <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
<para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
</para>
Added: trunk/packages/probcons/trunk/debian/probcons-extra.dirs
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-extra.dirs 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons-extra.dirs 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/doc
Added: trunk/packages/probcons/trunk/debian/probcons-extra.install
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-extra.install 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons-extra.install 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,4 @@
+pc-project usr/bin/
+pc-makegnuplot usr/bin/
+pc-compare usr/bin/
+
Added: trunk/packages/probcons/trunk/debian/probcons-extra.manpages
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-extra.manpages 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons-extra.manpages 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,3 @@
+debian/pc-makegnuplot.1
+debian/pc-compare.1
+debian/pc-project.1
Modified: trunk/packages/probcons/trunk/debian/probcons.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.1.xml 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons.1.xml 2006-06-04 15:13:27 UTC (rev 45)
@@ -176,7 +176,7 @@
<listitem><para>An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, probcons-RNA (1), is also distributed in the ProbCons Debian package.</para></listitem>
- <listitem><para>makegnufile (1), pc-compare (1), project (1), which are distributed together with probcons.</para></listitem>
+ <listitem><para>pc-makegnufile (1), pc-compare (1), pc-project (1), which are distributed separately in the probcons-extra package.</para></listitem>
</itemizedlist>
</refsect1>
@@ -188,7 +188,7 @@
<refsect1>
<title>AUTHORS</title>
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email>in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
+ <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
<para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
</para>
Added: trunk/packages/probcons/trunk/debian/probcons.copyright
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.copyright 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons.copyright 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,13 @@
+This package was debianized by Charles Plessy
+<charles-debian-nospam at plessy.org> on Wed, 3 May 2006. The packaging and the
+manpages work are in the public domain unless stated otherwise.
+
+ProbCons was downloaded from http://probcons.stanford.edu/probcons_v1_10.tar.gz
+The modified files for RNA alignment were downloaded from http://probcons.stanford.edu/probconsRNA.tar.gz
+The ProbCons manual was downloaded from http://probcons.stanford.edu/manual.pdf
+
+This software is in the public domain.
+
+ProbCons was written by by Chuong Do <chuongdo at cs.stanford.edu> in
+collaboration with Michael Brudno in the research group of Serafim Batzoglou,
+Department of Computer Science, Stanford University.
Added: trunk/packages/probcons/trunk/debian/probcons.dirs
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.dirs 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons.dirs 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/doc
+usr/share/doc/probcons
Added: trunk/packages/probcons/trunk/debian/probcons.docs
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.docs 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons.docs 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1 @@
+README
Added: trunk/packages/probcons/trunk/debian/probcons.install
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.install 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons.install 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,2 @@
+probcons usr/bin/
+probcons-RNA usr/bin/
Added: trunk/packages/probcons/trunk/debian/probcons.manpages
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.manpages 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/probcons.manpages 2006-06-04 15:13:27 UTC (rev 45)
@@ -0,0 +1,2 @@
+debian/probcons.1
+debian/probcons-RNA.1
Modified: trunk/packages/probcons/trunk/debian/rules
===================================================================
--- trunk/packages/probcons/trunk/debian/rules 2006-05-07 15:00:41 UTC (rev 44)
+++ trunk/packages/probcons/trunk/debian/rules 2006-06-04 15:13:27 UTC (rev 45)
@@ -12,7 +12,7 @@
BINARIES = probcons probcons-RNA project pc-compare makegnuplot
-MANPAGES = debian/probcons.1 debian/pc-compare.1 debian/project.1 debian/makegnuplot.1
+MANPAGES = debian/probcons.1 debian/probcons-RNA.1 debian/pc-compare.1 debian/pc-project.1 debian/pc-makegnuplot.1
DB2MAN = "/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl"
XP = xsltproc -o debian/ -''-nonet
@@ -26,7 +26,6 @@
dh_testdir
cp debian/Main-RNA.cc Main-RNA.cc
cp debian/Defaults-RNA.h Defaults-RNA.h
- uudecode debian/manual.pdf.ascii
$(MAKE)
touch build-stamp
@@ -38,24 +37,25 @@
dpatch deapply-all
rm -rf patch-stamp debian/patched
-manpages: debian/probcons.1.xml debian/probcons-RNA.1.xml debian/project.1.xml debian/pc-compare.1.xml debian/makegnuplot.1.xml
+manpages: debian/probcons.1.xml debian/probcons-RNA.1.xml debian/pc-project.1.xml debian/pc-compare.1.xml debian/pc-makegnuplot.1.xml
$(XP) $(DB2MAN) debian/probcons.1.xml
$(XP) $(DB2MAN) debian/probcons-RNA.1.xml
- $(XP) $(DB2MAN) debian/project.1.xml
+ $(XP) $(DB2MAN) debian/pc-project.1.xml
$(XP) $(DB2MAN) debian/pc-compare.1.xml
- $(XP) $(DB2MAN) debian/makegnuplot.1.xml
+ $(XP) $(DB2MAN) debian/pc-makegnuplot.1.xml
clean: unpatch
dh_testdir
dh_testroot
rm -f build-stamp configure-stamp
- dh_clean $(BINARIES) $(MANPAGES) Main-RNA.cc Defaults-RNA.h manual.pdf
+ dh_clean $(BINARIES) $(MANPAGES) Main-RNA.cc Defaults-RNA.h
install: build
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs
+ ln -s probcons debian/probcons-extra/usr/share/doc/probcons-extra
binary: build install
dh_testdir
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