Author: tille
Date: 2011-02-01 07:58:24 +0000 (Tue, 01 Feb 2011)
New Revision: 5841
Added:
trunk/packages/vienna-rna/trunk/debian/README.Source
trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base
Removed:
trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.docs
Modified:
trunk/packages/vienna-rna/trunk/debian/control
trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
trunk/packages/vienna-rna/trunk/debian/patches/series
trunk/packages/vienna-rna/trunk/debian/rules
trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install
Log:
Several documentation issues
Added: trunk/packages/vienna-rna/trunk/debian/README.Source
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/README.Source
(rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/README.Source 2011-02-01
07:58:24 UTC (rev 5841)
@@ -0,0 +1,14 @@
+The Source of ViennaRNA contains the following separate projects:
+
+ Readseq: A Recommends of the Debian packaged version of Readseq is used
+ and the patch which is applied in the Vienna RNA source to add
+ an additional output format is applied to the Debian packaged
+ version 1-9
+
+ RNAforester: Version 1.4 of this software is included in the Vienna RNA
+ source and it is used because it is not packaged for Debian.
+ The copy of the g2 library which is included in the source of
+ RNAforester is not used but the package is linked against the
+ Debian packaged version
+
+ -- Andreas Tille <ti...@debian.org> Tue, 01 Feb 2011 08:31:47 +0100
Modified: trunk/packages/vienna-rna/trunk/debian/control
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/control 2011-01-31 20:22:11 UTC
(rev 5840)
+++ trunk/packages/vienna-rna/trunk/debian/control 2011-02-01 07:58:24 UTC
(rev 5841)
@@ -5,7 +5,7 @@
Uploaders: Alex Mestiashvili <a...@biotec.tu-dresden.de>
DM-Upload-Allowed: yes
Build-Depends: debhelper (>= 7.1), autotools-dev, quilt (>= 0.47), tcsh | csh
| c-shel,
- libg2-dev, libgd2-xpm-dev, libx11-dev, texinfo, texlive-latex-base
+ libg2-dev, libgd2-xpm-dev, libx11-dev, texinfo, texlive-latex-base, help2man
Standards-Version: 3.9.1
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/vienna-rna/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/vienna-rna/trunk/
Modified: trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
2011-01-31 20:22:11 UTC (rev 5840)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
2011-02-01 07:58:24 UTC (rev 5841)
@@ -1,12 +1,14 @@
-Index: vienna-rna-1.8.4/man/RNAlib.texinfo
-===================================================================
---- vienna-rna-1.8.4.orig/man/RNAlib.texinfo 2011-01-30 17:38:00.000000000
+0000
-+++ vienna-rna-1.8.4/man/RNAlib.texinfo 2011-01-30 17:38:23.000000000
+0000
-@@ -17,6 +17,7 @@
- @title{Vienna RNA Package}
- @sp
- @subtitle{A Library for folding and comparing RNA secondary structures}
-+@dircategory science
-
- @vskip 0pt plus 1filll
- Copyright @copyright{1994-2002} @author{Ivo Hofacker and Peter Stadler}
+Author: Alex Mestiashvili <a...@biotec.tu-dresden.de>
+Date: 2011-01-30
+Description: texinfo needs "@directory Section" statement
+
+--- ViennaRNA-1.8.4.orig/man/RNAlib.texinfo
++++ ViennaRNA-1.8.4/man/RNAlib.texinfo
+@@ -3,6 +3,7 @@
+ @set revision $Id: RNAlib.texinfo,v 1.25 2009/01/13 17:49:58 ivo Exp $
+ @setfilename RNAlib.info
+ @settitle Vienna RNA Package
++@dircategory Science
+ @ifclear Version
+ @set Version 1.6
+ @end ifclear
Modified: trunk/packages/vienna-rna/trunk/debian/patches/series
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/series 2011-01-31
20:22:11 UTC (rev 5840)
+++ trunk/packages/vienna-rna/trunk/debian/patches/series 2011-02-01
07:58:24 UTC (rev 5841)
@@ -6,3 +6,4 @@
missing_x11.patch
fix_missing_header.patch
do_not_configure_g2-0.70.patch
+fix_RNAlib_info.patch
Modified: trunk/packages/vienna-rna/trunk/debian/rules
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/rules 2011-01-31 20:22:11 UTC
(rev 5840)
+++ trunk/packages/vienna-rna/trunk/debian/rules 2011-02-01 07:58:24 UTC
(rev 5841)
@@ -6,6 +6,9 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+pkg=vienna-rna
+DEB_COMPRESS_EXCLUDE := .pdf
+
%:
dh $@
@@ -43,5 +46,14 @@
override_dh_auto_install:
# rename perl scripts to remove the *.pl extension
- ls Utils/*.pl |while read line ; do cp $(CURDIR)/$$line
$(CURDIR)/debian/vienna-rna/usr/bin/`echo $$line |awk -F "/" '{print $$2}'|tr
-d '\.pl'` ; done
+ ls Utils/*.pl |while read line ; do cp $(CURDIR)/$$line
$(CURDIR)/debian/$(pkg)/usr/bin/`echo $$line |awk -F "/" '{print $$2}'|tr -d
'\.pl'` ; done
+ mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
+# for bin in RNAforester/src/RNAforester ; do \
+# echo "create manpage for `basename $${bin}`" ; \
+# help2man $(CURDIR)/$${bin} >
$(CURDIR)/debian/$(pkg)/usr/share/man/man1/`basename $${bin}`.1 ; \
+# done
+ # we need to provide proper name strings for individual manpages
+ help2man --name="aligning RNA secondary structures" \
+ $(CURDIR)/RNAforester/src/RNAforester >
$(CURDIR)/debian/$(pkg)/usr/share/man/man1/RNAforester.1
+
cd man; $(MAKE) pdf; $(MAKE) html
Added: trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base
(rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base
2011-02-01 07:58:24 UTC (rev 5841)
@@ -0,0 +1,25 @@
+Document: vienna-rna
+Title: Vienna RNA Package
+Author: Ivo Hofacker and Peter Stadler
+Abstract: RNA sequence analysis
+ RNA secondary structure prediction through energy minimization is the
+ most used function in the package. We provide three kinds of dynamic
+ programming algorithms for structure prediction: the minimum free energy
+ algorithm of (Zuker & Stiegler 1981) which yields a single optimal
+ structure, the partition function algorithm of (McCaskill 1990) which
+ calculates base pair probabilities in the thermodynamic ensemble, and
+ the suboptimal folding algorithm of (Wuchty et.al 1999) which generates
+ all suboptimal structures within a given energy range of the optimal
+ energy. For secondary structure comparison, the package contains several
+ measures of distance (dissimilarities) using either string alignment or
+ tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm
+ to design sequences with a predefined structure (inverse folding).
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/vienna-rna/html/*
+Index: /usr/share/doc/vienna-rna/html/index.html
+
+Format:pdf
+Files: /usr/share/doc/vienna-rna/RNAlib.pdf
+
Deleted: trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.docs
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.docs 2011-01-31
20:22:11 UTC (rev 5840)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.docs 2011-02-01
07:58:24 UTC (rev 5841)
@@ -1,2 +0,0 @@
-man/*.pdf
-
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install
2011-01-31 20:22:11 UTC (rev 5840)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install
2011-02-01 07:58:24 UTC (rev 5841)
@@ -1,2 +1,3 @@
-man/RNAlib.html usr/share/doc/vienna-rna/html
-Utils/Fold usr/share/doc/vienna-rna/examples
+man/RNAlib.html/* usr/share/doc/vienna-rna/html
+man/*.pdf usr/share/doc/vienna-rna
+Utils/Fold usr/share/doc/vienna-rna/examples
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