[med-svn] [snp-sites] 01/01: Man pages added to package creation using asciidoc. Most lintian issues resolved

[Jorge Soares]

This is an automated email from the git hooks/post-receive script.

jssoares-guest pushed a commit to branch master
in repository snp-sites.

commit bb7bf1fc74996cc325dd77e9605e3697b276a10d
Author: Jorge Soares <js21 at localhost.localdomain>
Date:   Thu Dec 19 10:21:58 2013 +0000

    Man pages added to package creation using asciidoc. Most lintian issues resolved
---
 Makefile.am                  |  1 +
 debian/control               | 14 +++++++++----
 debian/libsnp-sites1.install |  2 +-
 debian/rules                 | 10 +++++++++
 debian/snp-sites.manpages    |  1 +
 snp-sites.txt                | 50 ++++++++++++++++++++++++++++++++++++++++++++
 src/Makefile.am              |  1 +
 7 files changed, 74 insertions(+), 5 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 1bfdcf4..58d36a4 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1 +1,2 @@
 SUBDIRS=src
+ACLOCAL_AMFLAGS = -I m4
diff --git a/debian/control b/debian/control
index 9b6292e..d365348 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,12 @@ Build-Depends: debhelper (>= 8.0.0),
 	       autotools-dev,
 	       zlib1g-dev,
 	       check,
-	       dh-autoreconf
+	       dh-autoreconf,
+ 	       libxml2-utils,
+	       docbook,
+	       docbook-xsl,
+	       xsltproc,
+	       asciidoc
 Standards-Version: 3.9.3
 Homepage: https://github.com/sanger-pathogens/snp_sites
 Vcs-Git: git://anonscm.debian.org/debian-med/snp-sites.git
@@ -19,16 +24,17 @@ Depends: ${shlibs:Depends},
 	 ${misc:Depends},
 	 zlib1g,
 	 libsnp-sites1
-Description: snp-sites binary code
+Description: Binary code for the package snp-sites
  This program finds snp sites from a multi fasta alignment file
 
 Package: libsnp-sites1
 Architecture: any
+Pre-Depends: multiarch-support
 Section: libs
 Depends: ${shlibs:Depends},
 	 ${misc:Depends},
 	 zlib1g
-Description: snp-sites library code 
+Description: Run time libraries of the package snp-sites
  This program finds snp sites from a multi fasta alignment file
 
 Package: libsnp-sites1-dev
@@ -37,5 +43,5 @@ Section: libdevel
 Depends: ${shlibs:Depends},
 	 ${misc:Depends},
 	 libsnp-sites1 (= ${binary:Version})	
-Description: snp-sites development library code
+Description: Development libraries for the package snp-sites
  This program finds snp sites from a multi fasta alignment file
\ No newline at end of file
diff --git a/debian/libsnp-sites1.install b/debian/libsnp-sites1.install
index de3d642..3eee35c 100644
--- a/debian/libsnp-sites1.install
+++ b/debian/libsnp-sites1.install
@@ -1 +1 @@
-usr/lib/
\ No newline at end of file
+usr/lib/*/
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
index 85ce4e2..2735775 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,6 +8,16 @@
 
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
+export DH_ALWAYS_EXCLUDE=.gitignore
+
+mandir := $(CURDIR)/debian/man
+
 
 %:
 	dh $@ --with autoreconf
+
+override_dh_installman:
+	mkdir -p $(mandir)
+	a2x  --no-xmllint -f manpage $(CURDIR)/snp-sites.txt
+	mv $(CURDIR)/snp-sites.1 $(mandir)
+	dh_installman --
\ No newline at end of file
diff --git a/debian/snp-sites.manpages b/debian/snp-sites.manpages
new file mode 100644
index 0000000..d2c65e3
--- /dev/null
+++ b/debian/snp-sites.manpages
@@ -0,0 +1 @@
+debian/man/*
\ No newline at end of file
diff --git a/snp-sites.txt b/snp-sites.txt
new file mode 100644
index 0000000..de3d98f
--- /dev/null
+++ b/snp-sites.txt
@@ -0,0 +1,50 @@
+SNP-SITESDOC(1)
+==============
+:doctype: manpage
+
+
+NAME
+----
+snp-sites - finds snp sites from a multi fasta alignment file
+
+SYNOPSIS
+--------
+snp_sites [-mvph] [-o output_filename] [input file]
+
+DESCRIPTION
+-----------
+This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in the following formats:
+
+a multi fasta alignment, VCF, relaxed phylip format.
+
+OPTIONS
+-------
+*-m*::
+	Output a multi fasta alignment file (default)
+
+*-v*::
+	Output a VCF file
+
+*-p*::
+	Output a phylip file
+
+*-o*::
+	Specify an output filename
+
+*-h*::
+	This document
+
+EXAMPLES
+--------
+snp-sites my-alignment.aln
+
+snp-sites my-gzipped-alignment.aln.gz
+
+AUTHOR
+------
+Snp-sites was originally written by Andrew Page (ap13 at sanger.ac.uk)
+
+COPYING
+-------
+Wellcome Trust Sanger Institute Copyright (C) 2013 Wellcome Trust Sanger Institute
+This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
diff --git a/src/Makefile.am b/src/Makefile.am
index ddd0e04..d51dbf3 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,6 +1,7 @@
 # ship these headers in the "make dist" target
 dist_data_DATA = alignment-file.h  vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h parse-phylip.h string-cat.h kseq.h
 
+
 # snp_sites is our top level progra
 bin_PROGRAMS = snp-sites
 snp_sites_SOURCES = main.c

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.git