[med-svn] [pbbarcode] 02/03: Add manpage for pbbarcode

[Afif Elghraoui]

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

commit 954720b5a7b2ccb25488e297d023d2e6ddb40360
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Dec 18 22:03:00 2015 -0800

    Add manpage for pbbarcode
---
 debian/control                      |  1 +
 debian/patches/format-manpage.patch | 56 +++++++++++++++++++++++++++++++++++++
 debian/patches/series               |  1 +
 debian/rules                        |  9 +++++-
 4 files changed, 66 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 85c1c18..4670112 100644
--- a/debian/control
+++ b/debian/control
@@ -7,6 +7,7 @@ Build-Depends:
 	debhelper (>= 9),
 	dh-python,
 	python-setuptools,
+	python3-docutils,
 	python-all-dev,
 	python-pbcore,
 	python-numpy (>= 1.6.0),
diff --git a/debian/patches/format-manpage.patch b/debian/patches/format-manpage.patch
new file mode 100644
index 0000000..b12387c
--- /dev/null
+++ b/debian/patches/format-manpage.patch
@@ -0,0 +1,56 @@
+Description: Reformat upstream documentation into a manpage
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2015-12-18
+--- pbbarcode.orig/doc/PbbarcodeFunctionalSpecification.rst
++++ pbbarcode/doc/PbbarcodeFunctionalSpecification.rst
+@@ -1,17 +1,22 @@
+-.. pbbarcode Functional Specification
+-.. =======================================
++=========
++pbbarcode
++=========
+ 
+-.. Version
++---------------------------------------------------------
++annotate PacBio sequencing reads with barcode information
++---------------------------------------------------------
+ 
++:Date: December 2015
++:Manual section: 1
+ 
+-Introduction
+-````````````
+-This document describes the interface and input/output formats of the
+-``pbbarcode`` package command line tools. The package provides
++
++DESCRIPTION
++===========
++The **pbbarcode** package provides
+ utilities for annotating individual ZMWs directly from a bas.h5 file,
+ emitting fast[a|q] files for each barcode, labeling alignments stored
+ in a cmp.h5 file, and calling consensus on small amplicons (requires
+-``pbdagcon``)
++**pbdagcon**\ (1))
+ 
+ At the moment, Barcodes can be scored in two different ways:
+ ``symmetric`` and ``paired``. Symmetric mode supports barcode designs
+@@ -99,8 +104,7 @@
+   optional arguments:
+     -h, --help            show this help message and exit
+     --outDir OUTDIR       Where to write the newly created barcode.h5 files.
+-                          (default: /home/UNIXHOME/jbullard/projects/software/bi
+-                         oinformatics/tools/pbbarcode/doc)
++                          (default: /home/UNIXHOME/jbullard/projects/software/bioinformatics/tools/pbbarcode/doc)
+     --outFofn OUTFOFN     Write to outFofn (default: barcode.fofn)
+     --adapterSidePad ADAPTERSIDEPAD
+                           Pad with adapterSidePad bases (default: 4)
+@@ -120,7 +124,7 @@
+     --nProcs NPROCS       How many processes to use (default: 8)
+     --saveExtendedInfo    Whether to save extended information tothe barcode.h5
+                           files; this information is useful for debugging and
+-                                                  chimera detection (default: False)
++                          chimera detection (default: False)
+ 
+ The ``labelZmws`` command takes an input.fofn representing a set of
+ bas.h5 files to operate on. Additionally, it takes a barcode.fasta
diff --git a/debian/patches/series b/debian/patches/series
index f84d456..88aee25 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+format-manpage.patch
 module-multiarch-path.patch
diff --git a/debian/rules b/debian/rules
index 3ee9c45..10a1350 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,7 +2,7 @@
 
 #DH_VERBOSE = 1
 
-#include /usr/share/dpkg/default.mk
+include /usr/share/dpkg/default.mk
 
 PYBUILD_NAME = pbbarcode
 
@@ -13,3 +13,10 @@ override_dh_auto_test:
 	PYBUILD_SYSTEM=custom \
 	PYBUILD_TEST_ARGS="find tests -name '*.py' | xargs nosetests -v" \
 	dh_auto_test
+
+override_dh_install:
+	mkdir -p debian/$(DEB_SOURCE)/usr/share/man/man1
+	rst2man --quiet \
+	doc/PbbarcodeFunctionalSpecification.rst \
+	> debian/$(DEB_SOURCE)/usr/share/man/man1/pbbarcode.1
+	dh_install

-- 
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