[med-svn] [fast5] 02/02: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Jan 19 09:16:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository fast5.
commit d9de39a2e9f65535cc13e082c9e4e3a47375eb3a
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Tue Jan 19 01:08:50 2016 -0800
Initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 24 ++++++++++++++++++++++++
debian/copyright | 34 ++++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/examples | 2 ++
debian/install | 2 ++
debian/patches/relative-paths.patch | 17 +++++++++++++++++
debian/patches/revise-example.patch | 31 +++++++++++++++++++++++++++++++
debian/patches/series | 2 ++
debian/rules | 7 +++++++
debian/source/format | 1 +
debian/tests/control | 6 ++++++
debian/watch | 4 ++++
14 files changed, 137 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..06cd251
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+fast5 (0~20150918-1) UNRELEASED; urgency=low
+
+ * Initial release - upstream git revision 0639cc5 (Closes: #811460)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Mon, 18 Jan 2016 14:26:27 -0800
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b864d56
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: fast5
+Section: libs
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Afif Elghraoui <afif at ghraoui.name>,
+Build-Depends:
+ debhelper (>= 9),
+Standards-Version: 3.9.6
+Homepage: https://github.com/mateidavid/fast5
+Vcs-Git: git://anonscm.debian.org/debian-med/fast5.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/fast5.git
+
+Package: libfast5-dev
+Section: libdevel
+Architecture: all
+Depends:
+ ${misc:Depends},
+ libhdf5-dev | libhdf5-mpich-dev | libhdf5-openmpi-dev,
+Description: library for reading Oxford Nanopore Fast5 files -- headers
+ A lightweight C++11 library to read raw signal data from Oxford
+ Nanopore's FAST5 files.
+ .
+ This package provides the header files for development with fast5.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..29623a2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,34 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: fast5
+Source: https://github.com/mateidavid/fast5
+
+Files: *
+Copyright: 2015 Matei David
+License: MIT
+Comment:
+ Licensing terms are mentioned on https://github.com/mateidavid/fast5/issues/7#issuecomment-172662247
+ and are expected to be noted in the source distribution in future upstream
+ revisions.
+
+Files: debian/*
+Copyright: 2016 Afif Elghraoui <afif at ghraoui.name>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..19bfbca
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,2 @@
+src/a.cpp
+src/Makefile
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..3662190
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+src/fast5.hpp usr/include
+src/hdf5_tools.hpp usr/include/fast5
diff --git a/debian/patches/relative-paths.patch b/debian/patches/relative-paths.patch
new file mode 100644
index 0000000..9635c69
--- /dev/null
+++ b/debian/patches/relative-paths.patch
@@ -0,0 +1,17 @@
+Description: Adjust include statement for relocation of auxiliary header
+ Moving the auxiliary header file to a subdirectory of usr/include
+ requires modifying the include statement in fast5.hpp.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2016-01-19
+--- fast5.orig/src/fast5.hpp
++++ fast5/src/fast5.hpp
+@@ -9,7 +9,7 @@
+ #include <string>
+ #include <vector>
+
+-#include "hdf5_tools.hpp"
++#include <fast5/hdf5_tools.hpp>
+ #define MAX_K_LEN 8
+
+ namespace fast5
diff --git a/debian/patches/revise-example.patch b/debian/patches/revise-example.patch
new file mode 100644
index 0000000..9b68f09
--- /dev/null
+++ b/debian/patches/revise-example.patch
@@ -0,0 +1,31 @@
+Description: Revise example as applicable for Debian.
+ The main changes are to find the hdf5 libraries as they are
+ installed by the Debian package.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2016-01-19
+--- fast5.orig/src/Makefile
++++ fast5/src/Makefile
+@@ -1,2 +1,9 @@
+-a: a.cpp fast5.hpp hdf5_tools.hpp
+- g++ -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -pedantic -Wno-unused-parameter -o $@ $^ -L /usr/local/lib -lhdf5
++
++a: a.cpp
++ h5c++ -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -pedantic -Wno-unused-parameter -o $@ -lhdf5
++
++
++clean:
++ $(RM) a
++
++.PHONY: clean
+--- fast5.orig/src/a.cpp
++++ fast5/src/a.cpp
+@@ -2,7 +2,7 @@
+ #include <iostream>
+ #include <string>
+
+-#include "fast5.hpp"
++#include <fast5.hpp>
+
+ using namespace std;
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..d2834ed
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+relative-paths.patch
+revise-example.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..3d2f40f
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+#include /usr/share/dpkg/default.mk
+
+%:
+ dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..7f891c9
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,6 @@
+Test-Command: cd src && make; make clean
+Depends:
+ @,
+ make,
+Restrictions:
+ rw-build-tree,
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..d145556
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+# Upstream has no formal releases for this project. We update this
+# as needed for nanopolish (where it's bundled)
--
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