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commit 534bc885122d315001bb8fb1c72ec27ce34a670c
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Sep 5 20:31:27 2015 -0700
Build documentation package
---
debian/control | 17 +++++++++++++++++
debian/patches/make-doc | 16 ++++++++++++++++
debian/patches/series | 1 +
debian/python-pbalign-doc.doc-base | 8 ++++++++
debian/python-pbalign-doc.install | 1 +
debian/python-pbalign-doc.links | 2 ++
debian/rules | 4 ++++
7 files changed, 49 insertions(+)
diff --git a/debian/control b/debian/control
index 7eb838c..8e21cc9 100644
--- a/debian/control
+++ b/debian/control
@@ -8,6 +8,7 @@ Build-Depends: debhelper (>= 9),
python-all,
python-setuptools,
python-pbcore (>= 0.8.5),
+ python-sphinx,
help2man,
python-pkg-resources,
blasr
@@ -24,6 +25,7 @@ Depends: ${misc:Depends},
blasr
Recommends: python-pbh5tools,
hdf5-tools
+Suggests: python-pbalign-doc
Description: map Pacific Biosciences reads to reference DNA sequences
pbalign aligns PacBio reads to reference sequences, filters aligned
reads according to user-specific filtering criteria, and converts the
@@ -31,3 +33,18 @@ Description: map Pacific Biosciences reads to reference DNA sequences
format.
.
This package is part of the SMRTAnalysis suite.
+
+Package: python-pbalign-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends},
+ libjs-jquery,
+ libjs-underscore
+Description: API documentation for python-pbalign
+ pbalign aligns PacBio reads to reference sequences, filters aligned
+ reads according to user-specific filtering criteria, and converts the
+ output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5)
+ format.
+ .
+ pbalign is part of the SMRTAnalysis suite. This package contains the
+ API documentation
diff --git a/debian/patches/make-doc b/debian/patches/make-doc
new file mode 100644
index 0000000..68e14d3
--- /dev/null
+++ b/debian/patches/make-doc
@@ -0,0 +1,16 @@
+Description: Fix source folder name in Makefile
+ The sphinx-apidoc call targets a nonexistent src/ folder
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: https://github.com/PacificBiosciences/pbalign/pull/12
+Last-Update: 2015-09-05
+--- python-pbalign.orig/Makefile
++++ python-pbalign/Makefile
+@@ -23,7 +23,7 @@
+ find tests/cram -name "*.t" | xargs cram
+
+ doc:
+- sphinx-apidoc -T -f -o doc src/ && cd doc && make html
++ sphinx-apidoc -T -f -o doc pbalign/ && cd doc && make html
+
+ docs: doc
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..9a44084
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+make-doc
diff --git a/debian/python-pbalign-doc.doc-base b/debian/python-pbalign-doc.doc-base
new file mode 100644
index 0000000..4f1d055
--- /dev/null
+++ b/debian/python-pbalign-doc.doc-base
@@ -0,0 +1,8 @@
+Document: python-pbalign
+Title: Pacific Biosciences pbalign documentation
+Author: Pacific Biosciences
+Section: Programming/Python
+
+Format: HTML
+Index: /usr/share/doc/python-pbalign/html/index.html
+Files: /usr/share/doc/python-pbalign/html/*.html
diff --git a/debian/python-pbalign-doc.install b/debian/python-pbalign-doc.install
new file mode 100644
index 0000000..c02b6d5
--- /dev/null
+++ b/debian/python-pbalign-doc.install
@@ -0,0 +1 @@
+doc/_build/html usr/share/doc/python-pbalign
diff --git a/debian/python-pbalign-doc.links b/debian/python-pbalign-doc.links
new file mode 100644
index 0000000..e4b52f0
--- /dev/null
+++ b/debian/python-pbalign-doc.links
@@ -0,0 +1,2 @@
+/usr/share/javascript/jquery/jquery.js /usr/share/doc/python-pbalign/html/_static/jquery.js
+/usr/share/javascript/underscore/underscore.js /usr/share/doc/python-pbalign/html/_static/underscore.js
diff --git a/debian/rules b/debian/rules
index 12a6d44..c84ff0b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -15,6 +15,10 @@ MANDIR = $(BUILDDIR)/usr/share/man/man1
%:
LC_ALL=C.UTF-8 dh $@ --with=python2 --buildsystem=pybuild
+override_dh_auto_build:
+ dh_auto_build
+ $(MAKE) doc
+
override_dh_install: SHELL=bash
override_dh_install:
dh_install
--
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