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 <[email protected]> + + + +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 <[email protected]> Uploaders: Alex Mestiashvili <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
