[med-svn] [pbgenomicconsensus] 01/01: Generate a manpage from one of the documentation files

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository pbgenomicconsensus.

commit d7d9eb572477a9a56023fe4f480ef945c0ecfea8
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Oct 7 02:09:53 2015 -0700

    Generate a manpage from one of the documentation files
    
    One of the rst files in doc/ describes a file format. This commit
    sets it up so that it becomes a man page in section 5.
---
 debian/control                |  1 +
 debian/patches/manpages.patch | 52 +++++++++++++++++++++++++++++++++++++++++++
 debian/patches/series         |  1 +
 debian/rules                  |  6 +++++
 4 files changed, 60 insertions(+)

diff --git a/debian/control b/debian/control
index b88a18a..1e256f7 100644
--- a/debian/control
+++ b/debian/control
@@ -5,6 +5,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif at ghraoui.name>
 Build-Depends: debhelper (>= 9),
 	       dh-python,
+	       rst2man,
 	       python-all,
 	       python-setuptools,
 	       python-pbconsensuscore,
diff --git a/debian/patches/manpages.patch b/debian/patches/manpages.patch
new file mode 100644
index 0000000..0898f29
--- /dev/null
+++ b/debian/patches/manpages.patch
@@ -0,0 +1,52 @@
+Description: Turn upstream file format documentation into a manpage
+ These patches change the rst file to be suitable input to rst2man.
+ I followed the example at
+ http://docutils.sourceforge.net/sandbox/manpage-writer/rst2man.txt
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2015-10-06
+--- pbgenomicconsensus.orig/doc/VariantsGffSpecification.rst
++++ pbgenomicconsensus/doc/VariantsGffSpecification.rst
+@@ -1,6 +1,20 @@
++=====
++pbgff
++=====
++
++----------------------------------------------
++Pacific Biosciences extended GFFv3 file format
++----------------------------------------------
++
++:Author: Pacific Biosciences <devnet at pacificbiosciences.com>
++:Date: August 2014
++:Version: 2.1
++:Manual section: 5
++:Manual group: Bioinformatics formats
+ 
+-``variants.gff`` File Format (Version 2.1)
+-============================================
++
++DESCRIPTION
++===========
+ 
+ As of this version, ``variants.gff`` is our primary variant call file
+ format.  The ``variants.gff`` file is based on the `GFFv3 standard`_.
+@@ -40,7 +54,7 @@
+ ``pacbio-variant-version`` reflects the specification version that the
+ file contents should adhere to.
+ 
+-  The ``sequence-region`` headers describe the names and extents of
++The ``sequence-region`` headers describe the names and extents of
+ the reference groups (i.e. reference contigs) that will be refered to
+ in the file.  The names are the same as the full FASTA header.
+ 
+@@ -162,8 +176,8 @@
+ the variant file should be able to read it in either form.
+ 
+ 
+-Other file formats
+-------------------
++SEE ALSO
++========
+ 
+ The VCF and BED standards describe variant-call specific file formats.
+ We can currently translate `variants.gff` files to these formats, but
diff --git a/debian/patches/series b/debian/patches/series
index 65d11d4..2ea9908 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 python-scripts
+manpages.patch
diff --git a/debian/rules b/debian/rules
index 9226733..9bb6a3c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,10 +6,16 @@ include /usr/share/dpkg/default.mk
 
 export PYBUILD_NAME := $(DEB_SOURCE)
 BINDIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
+MANDIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/
 
 %:
 	LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
 
+override_dh_auto_build:
+	dh_auto_build
+	mkdir -p $(MANDIR)/man5
+	rst2man doc/VariantsGffSpecification.rst > $(MANDIR)/man5/pbgff.5
+
 override_dh_install:
 	dh_install
 	for script in $(BINDIR)/*.py; \

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