[med-svn] r4078 - in trunk/packages/last-align/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Sep 29 21:27:48 UTC 2009
Author: tille
Date: 2009-09-29 21:27:48 +0000 (Tue, 29 Sep 2009)
New Revision: 4078
Added:
trunk/packages/last-align/trunk/debian/dirs
trunk/packages/last-align/trunk/debian/patches/
trunk/packages/last-align/trunk/debian/patches/20_help_output_2_stdout.patch
trunk/packages/last-align/trunk/debian/patches/series
Modified:
trunk/packages/last-align/trunk/debian/changelog
trunk/packages/last-align/trunk/debian/control
trunk/packages/last-align/trunk/debian/rules
Log:
Trying to create manpages via help2man wherever possible
Modified: trunk/packages/last-align/trunk/debian/changelog
===================================================================
--- trunk/packages/last-align/trunk/debian/changelog 2009-09-29 19:33:39 UTC (rev 4077)
+++ trunk/packages/last-align/trunk/debian/changelog 2009-09-29 21:27:48 UTC (rev 4078)
@@ -1,3 +1,16 @@
+last-align (62-1) unstable; urgency=low
+
+ * New upstream version
+ * debian/control:
+ - Added myself to upstream
+ - Standards-Version: 3.8.3
+ - BUild-Depends: help2man, quilt
+ * debian/rules: Try to create manpages via help2man wherever possible
+ * debian/patches: Make sure help output goes to stdout as GNU coding
+ style suggests and is needed by help2man
+
+ -- Andreas Tille <tille at debian.org> Tue, 29 Sep 2009 13:38:57 +0200
+
last-align (58-1) unstable; urgency=low
* New upstream release able to use sequence quality scores.
Modified: trunk/packages/last-align/trunk/debian/control
===================================================================
--- trunk/packages/last-align/trunk/debian/control 2009-09-29 19:33:39 UTC (rev 4077)
+++ trunk/packages/last-align/trunk/debian/control 2009-09-29 21:27:48 UTC (rev 4078)
@@ -3,9 +3,10 @@
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7), cdbs
-Standards-Version: 3.8.1
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7), cdbs, help2man, quilt
+Standards-Version: 3.8.3
Homepage: http://last.cbrc.jp/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/last-align/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/last-align/trunk/
Added: trunk/packages/last-align/trunk/debian/dirs
===================================================================
--- trunk/packages/last-align/trunk/debian/dirs (rev 0)
+++ trunk/packages/last-align/trunk/debian/dirs 2009-09-29 21:27:48 UTC (rev 4078)
@@ -0,0 +1 @@
+/usr/share/man/man1/
Added: trunk/packages/last-align/trunk/debian/patches/20_help_output_2_stdout.patch
===================================================================
--- trunk/packages/last-align/trunk/debian/patches/20_help_output_2_stdout.patch (rev 0)
+++ trunk/packages/last-align/trunk/debian/patches/20_help_output_2_stdout.patch 2009-09-29 21:27:48 UTC (rev 4078)
@@ -0,0 +1,56 @@
+Author: Andreas Tille <tille at debian.org>
+Description: According to GNU coding standards help messages should go to stdout
+ not to stderr. THis patch ensures that help2man will work correctly
+--- last-62.orig/src/LastalArguments.cc
++++ last-62/src/LastalArguments.cc
+@@ -4,6 +4,8 @@
+ #include "stringify.hh"
+ #include <unistd.h> // getopt
+ #include <sstream>
++#include <cstdlib>
++#include <iostream>
+ #include <vector>
+ #include <stdexcept>
+ #include <cstring> // strtok
+@@ -108,7 +110,8 @@
+ != -1 ){
+ switch(c){
+ case 'h':
+- throw std::runtime_error(help);
++ std::cout << help ;
++ exit(1);
+ case 'o':
+ outFile = optarg;
+ break;
+--- last-62.orig/src/LastdbArguments.cc
++++ last-62/src/LastdbArguments.cc
+@@ -2,6 +2,8 @@
+
+ #include "LastdbArguments.hh"
+ #include "stringify.hh"
++#include <cstdlib>
++#include <iostream>
+ #include <unistd.h> // getopt
+ #include <stdexcept>
+
+@@ -27,6 +29,7 @@
+ usage: lastdb [options] output-name fasta-sequence-file(s)\n\
+ \n\
+ Main Options (default settings):\n\
++-h: show all options and their default settings\n\
+ -p: interpret the sequences as proteins\n\
+ -c: read the sequences case-sensitively\n\
+ -m: periodic spaced-seed pattern (" + maskPattern + ")\n\
+@@ -40,8 +43,11 @@
+ ";
+
+ int c;
+- while( (c = getopt(argc, argv, "pcm:w:s:a:b:v")) != -1 ) {
++ while( (c = getopt(argc, argv, "hpcm:w:s:a:b:v")) != -1 ) {
+ switch(c){
++ case 'h':
++ std::cout << usage;
++ exit(1);
+ case 'p':
+ isProtein = true;
+ break;
Added: trunk/packages/last-align/trunk/debian/patches/series
===================================================================
--- trunk/packages/last-align/trunk/debian/patches/series (rev 0)
+++ trunk/packages/last-align/trunk/debian/patches/series 2009-09-29 21:27:48 UTC (rev 4078)
@@ -0,0 +1 @@
+20_help_output_2_stdout.patch
Modified: trunk/packages/last-align/trunk/debian/rules
===================================================================
--- trunk/packages/last-align/trunk/debian/rules 2009-09-29 19:33:39 UTC (rev 4077)
+++ trunk/packages/last-align/trunk/debian/rules 2009-09-29 21:27:48 UTC (rev 4078)
@@ -7,21 +7,44 @@
# http://debian-med.alioth.debian.org/docs/policy.html
include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
include /usr/share/cdbs/1/class/makefile.mk
DEB_MAKE_BUILD_TARGET = --directory src
+pkg=last-align
+version=$(shell dpkg-parsechangelog | grep "^Version:" | sed -e "s/^Version:[[:space:]]\+\([\.0-9]*\)-[0-9]\+[[:space:]]*/\1/" )
+
clean::
$(RM) src/lastdb src/lastal src/*.o
-binary-fixup/last-align::
- prename 's/.py$$//' debian/last-align/usr/bin/*py
- prename 's/.sh$$//' debian/last-align/usr/bin/*sh
- mv debian/last-align/usr/share/doc/last-align/ChangeLog.txt.gz debian/last-align/usr/share/doc/last-align/changelog.gz
+binary-fixup/$(pkg)::
+ prename 's/.py$$//' debian/$(pkg)/usr/bin/*py
+ prename 's/.sh$$//' debian/$(pkg)/usr/bin/*sh
+ mv debian/$(pkg)/usr/share/doc/$(pkg)/ChangeLog.txt.gz debian/$(pkg)/usr/share/doc/$(pkg)/changelog.gz
+ # try to create man pages whereever possible
+ help2man --no-info --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
+ --version-string="$(version)" \
+ $(CURDIR)/scripts/last-dotplot.py > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/last-dotplot.1
+ help2man --no-info --name="genome-scale comparison of biological sequences" \
+ --version-string="$(version)" --help-option="-h" \
+ $(CURDIR)/src/lastal > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/lastal.1
+ help2man --no-info --name="genome-scale comparison of biological sequences" \
+ --version-string="$(version)" --help-option="-h" \
+ $(CURDIR)/src/lastdb > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/lastdb.1
+ help2man --no-info --version-string="$(version)" \
+ --name="Sort MAF-format alignments by sequence name" \
+ $(CURDIR)/scripts/maf-sort.sh > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/maf-sort.1
+ help2man --no-info --version-string="$(version)" \
+ --name="changes the order of the sequences in MAF-format alignments" \
+ $(CURDIR)/scripts/maf-swap.py > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/maf-swap.1
+ help2man --no-info --version-string="$(version)" \
+ --name=" " \
+ $(CURDIR)/scripts/maf2html.py > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/maf2html.1
# The unzip command from the unzip package is needed for this one.
# Please update debian/changelog before calling this target.
get-orig-source:
[ -f ../last-$(DEB_UPSTREAM_VERSION).zip ] || uscan --force-download
unzip ../last-$(DEB_UPSTREAM_VERSION).zip -d..
- tar --create --gzip --file ../last-align_$(DEB_UPSTREAM_VERSION).orig.tar.gz ../last-$(DEB_UPSTREAM_VERSION)
+ tar --create --gzip --file ../$(pkg)_$(DEB_UPSTREAM_VERSION).orig.tar.gz ../last-$(DEB_UPSTREAM_VERSION)
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