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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: + Afif Elghraoui <[email protected]>, +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: <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbdagcon.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
