[med-svn] [pbdagcon] 02/02: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sat Nov 28 20:44:12 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository pbdagcon.
commit 08cb4c9a1a45c0237481a5a88694c9d2b228f72b
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Nov 28 12:42:50 2015 -0800
Initial packaging
---
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 43 ++++++++++++++++++++++++++++++++++
debian/copyright | 47 ++++++++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/examples | 4 ++++
debian/install | 1 +
debian/patches/external-libs.patch | 29 +++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 12 ++++++++++
debian/source/format | 1 +
debian/watch | 3 +++
12 files changed, 148 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e309228
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pbdagcon (0~20151114+git1d12e13+ds-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #796644)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Fri, 27 Nov 2015 15:40:43 -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..257b7c4
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,43 @@
+Source: pbdagcon
+Section: science
+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),
+ libboost-dev,
+ libtclap-dev,
+ libpbseq-dev,
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/pbdagcon
+Vcs-Git: git://anonscm.debian.org/debian-med/pbdagcon.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/pbdagcon.git
+
+Package: pbdagcon
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ libpbdata,
+ libblasr,
+Description: sequence consensus using directed acyclic graphs
+ pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
+ which is a sequence consensus algorithm based on using directed acyclic
+ graphs to encode multiple sequence alignment.
+ .
+ It uses the alignment information from blasr to align sequence reads to a
+ "backbone" sequence. Based on the underlying alignment directed acyclic graph
+ (DAG), it will be able to use the new information from the reads to find the
+ discrepancies between the reads and the "backbone" sequences. A dynamic
+ programming process is then applied to the DAG to find the optimum sequence
+ of bases as the consensus. The new consensus can be used as a new backbone
+ sequence to iteratively improve the consensus quality.
+ .
+ While the code is developed for processing PacBio(TM) raw sequence data,
+ the algorithm can be used for general consensus purpose. Currently, it only
+ takes FASTA input. For shorter read sequences, one might need to adjust the
+ blasr alignment parameters to get the alignment string properly.
+ .
+ The code and the underlying graphical data structure have been used for some
+ algorithm development prototyping including phasing reads and pre-assembly.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..83a035c
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,47 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pbdagcon
+Upstream-Contact: <devnet at pacificbiosciences.com>
+Source: https://github.com/PacificBiosciences/pbdagcon
+Files-Excluded: src/cpp/third-party/tclap/*
+
+Files: *
+Copyright: 2011-2015 Pacific Biosciences of California, Inc.
+License: PacBio-BSD-3-Clause
+
+Files: src/cpp/third-party/easylogging++.h
+Copyright: TODO
+License: TODO
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: PacBio-BSD-3-Clause
+
+License: PacBio-BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted (subject to the limitations in the
+ disclaimer below) provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ * Neither the name of Pacific Biosciences nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ .
+ NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+ GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+ BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
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..838d476
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,4 @@
+src/filterm4.py
+src/m4topre.py
+src/q-sense.py
+src/pbdagcon_wf.sh
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..4a0c2e5
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+src/cpp/pbdagcon usr/bin
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
new file mode 100644
index 0000000..12ed885
--- /dev/null
+++ b/debian/patches/external-libs.patch
@@ -0,0 +1,29 @@
+Description: Allow library paths to be overridden externally
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-11-27
+--- pbdagcon.orig/Makefile
++++ pbdagcon/Makefile
+@@ -1,6 +1,9 @@
+ .PHONY: all clean test init-submodule cpp-github cpp cpp-check cpp-clean
+ SHELL = /bin/bash -e
+
++export BLASR ?= $(PWD)/blasr_libcpp/alignment
++export PBDATA ?= $(PWD)/blasr_libcpp/pbdata
++
+ all: cpp-github
+
+ clean: cpp-clean
+@@ -27,10 +30,10 @@
+
+ # C++ project build directives
+ cpp-github:
+- $(MAKE) -C src/cpp BLASR=$(PWD)/blasr_libcpp/alignment PBDATA=$(PWD)/blasr_libcpp/pbdata
++ $(MAKE) -C src/cpp
+
+ cpp-github-check:
+- $(MAKE) -C test/cpp BLASR=$(PWD)/blasr_libcpp/alignment PBDATA=$(PWD)/blasr_libcpp/pbdata
++ $(MAKE) -C test/cpp
+
+ cpp:
+ $(MAKE) -C src/cpp
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7e67dce
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+external-libs.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..65711d4
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,12 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+
+export boost := /usr/include/boost
+export BLASR := /usr/include/blasr
+export PBDATA := /usr/include/pbdata
+
+%:
+ dh $@ --parallel
+
+override_dh_auto_test: ;
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/watch b/debian/watch
new file mode 100644
index 0000000..763d56c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+# There are no formal upstream releases
--
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