[med-svn] r5843 - trunk/packages/vienna-rna/trunk/debian
Andreas Tille
tille at alioth.debian.org
Tue Feb 1 18:48:44 UTC 2011
Author: tille
Date: 2011-02-01 18:48:37 +0000 (Tue, 01 Feb 2011)
New Revision: 5843
Added:
trunk/packages/vienna-rna/trunk/debian/b2ct.1
Modified:
trunk/packages/vienna-rna/trunk/debian/control
trunk/packages/vienna-rna/trunk/debian/rules
trunk/packages/vienna-rna/trunk/debian/vienna-rna.dirs
trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
trunk/packages/vienna-rna/trunk/debian/vienna-rna.lintian-overrides
trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages
Log:
Continue working on the docs via help2man, perldoc and texinfo
Added: trunk/packages/vienna-rna/trunk/debian/b2ct.1
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/b2ct.1 (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/b2ct.1 2011-02-01 18:48:37 UTC (rev 5843)
@@ -0,0 +1,25 @@
+.TH B2CT "1" User Contributed Perl Documentation
+
+.SH NAME
+b2ct \- converts the bracket notation produced by RNAfold into an '.ct' file
+
+.SH SYNOPSIS
+b2ct < structure_file > ct_file.ct
+
+.SH DESCRIPTION
+This program converts the bracket notation for RNA secondary structures
+produced by RNAfold to .ct files used by Michael Zukers Program.
+
+In conection with RNAfold it can be used as
+ RNAfold < sequence_file | b2ct > ct_file.ct
+
+.SH SEE ALSO
+
+RNAFOld(1)
+
+.SH AUTHOR
+ Ivo L. Hofacker <ivo at tbi.univie.ac.at>
+
+
+
+perl v5.10.1 2011-02-01
Modified: trunk/packages/vienna-rna/trunk/debian/control
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/control 2011-02-01 16:41:04 UTC (rev 5842)
+++ trunk/packages/vienna-rna/trunk/debian/control 2011-02-01 18:48:37 UTC (rev 5843)
@@ -4,8 +4,8 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Alex Mestiashvili <alex at 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, help2man
+Build-Depends: debhelper (>= 7.1), autotools-dev, quilt (>= 0.47),
+ libg2-dev, libgd2-xpm-dev, libx11-dev, texinfo, texlive-latex-base, help2man, perl-doc
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/rules
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/rules 2011-02-01 16:41:04 UTC (rev 5842)
+++ trunk/packages/vienna-rna/trunk/debian/rules 2011-02-01 18:48:37 UTC (rev 5843)
@@ -16,21 +16,6 @@
dh_auto_configure -- --with-cluster
override_dh_auto_clean:
-### <begin-just-remove>
- ## (at) Removing packages from build directory which are inside the tarball is
- ## wrong. Either remove it straight in the tarball or just leave them
- ## untouched. Rationale: After 'make -f debian/rules clean` the build
- ## directory should be *identical* to the tarball and there should not some
- ## files missing.
- # rm -f build-arch-stamp build-indep-stamp
- # libg2-dev is standalone package
- # rm -rf RNAforester/g2-0.70
- # readseq is standalone package
- # rm -rf Readseq
-
- ### (at) hmmmm, these files are in the upstream tarball and removing them doese not seem to be a good idea
- # rm -f config.sub config.guess
-### <end-just-remove>
echo "Do not run dh_auto_clean because it forces removal of man pages"
override_dh_clean:
@@ -45,15 +30,32 @@
cd Perl; [ ! -f Makefile ] || $(MAKE) distclean; rm -f *.old *.ps test.coord test.par
override_dh_auto_install:
- # rename perl scripts to remove the *.pl extension
- 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}`" ; \
+ # rename perl scripts to remove the *.pl extension and create manpage via perldoc
+ for script in `ls Utils/*.pl` ; do \
+ newscript=`basename $${script} .pl` ; \
+ cp -a $${script} $(CURDIR)/debian/$(pkg)/usr/bin/$${newscript} ; \
+ perldoc -oman -F $${script} | \
+ sed -e "s/$${newscript}\.pl/$${newscript}/g" \
+ -e "s/$${newscript} *- */$${newscript} \\- /g" \
+ -e "s/^[A-Z]/.SH &/" -e "1s/^.SH/.TH/" \
+ -e "s/\(.TH $${newscript}\)(1) *\(.*[^ ]\) *$${newscript}.*/\1 \"1\" \"\2\"/i" \
+ -e "s/^ *//" \
+ > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${newscript}.1 ; \
+ if [ ! -s $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${newscript}.1 ] ; then \
+ rm -f $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${newscript}.1 ; \
+ fi ; \
+ done
+ # Create manpages which have proper name entries in --help output
+# for bin in Kinfold/Kinfold ; do \
# help2man $(CURDIR)/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/`basename $${bin}`.1 ; \
# done
- # we need to provide proper name strings for individual manpages
+ # Create manpages which 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
+ help2man --name="Kinetic Folding Program for Nucleic Acids" \
+ $(CURDIR)/Kinfold/Kinfold > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/Kinfold.1
cd man; $(MAKE) pdf; $(MAKE) html
+
+override_dh_compress:
+ dh_compress --exclude=.pdf
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna.dirs
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.dirs 2011-02-01 16:41:04 UTC (rev 5842)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.dirs 2011-02-01 18:48:37 UTC (rev 5843)
@@ -1 +1,2 @@
usr/bin
+usr/share/man/man1
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.install 2011-02-01 16:41:04 UTC (rev 5842)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.install 2011-02-01 18:48:37 UTC (rev 5843)
@@ -20,14 +20,3 @@
RNAforester/src/RNAforester usr/bin
Utils/b2ct usr/bin
Utils/popt usr/bin
-#Utils/b2mt usr/bin
-#Utils/cmount usr/bin
-#Utils/coloraln usr/bin
-#Utils/colorrna usr/bin
-#Utils/ct2b usr/bin
-#Utils/dpzoom usr/bin
-#Utils/Fold usr/bin # moved to examples
-#Utils/mountain usr/bin
-#Utils/refold usr/bin
-#Utils/relplot usr/bin
-#Utils/rotate_ss usr/bin
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna.lintian-overrides
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.lintian-overrides 2011-02-01 16:41:04 UTC (rev 5842)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.lintian-overrides 2011-02-01 18:48:37 UTC (rev 5843)
@@ -2,3 +2,6 @@
# reason to repack the tarball
vienna-rna source: configure-generated-file-in-source RNAforester/g2-0.70/config.log
vienna-rna source: configure-generated-file-in-source RNAforester/g2-0.70/config.status
+
+# The line is not intended to be broken
+vienna-rna: manpage-has-errors-from-man usr/share/man/man1/RNAup.1.gz 140: warning [p 3, 1.0i]: can't break line
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages 2011-02-01 16:41:04 UTC (rev 5842)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages 2011-02-01 18:48:37 UTC (rev 5843)
@@ -1 +1,2 @@
man/*.1
+debian/*.1
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