[med-svn] [nanocall] 02/02: Add initial packaging, does not build (see upstream issue #9)
Andreas Tille
tille at debian.org
Tue Sep 13 13:25:17 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository nanocall.
commit 2ba59910f9b162bcebd599ab3c9d00c88d75c1a4
Author: Andreas Tille <tille at debian.org>
Date: Tue Sep 13 15:20:02 2016 +0200
Add initial packaging, does not build (see upstream issue #9)
---
debian/changelog | 6 ++++
debian/compat | 1 +
debian/control | 42 ++++++++++++++++++++++++
debian/copyright | 51 +++++++++++++++++++++++++++++
debian/patches/remove_broken_makefile.patch | 42 ++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 23 +++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 9 +++++
debian/watch | 3 ++
10 files changed, 179 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..4901a14
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+nanocall (0.6.14-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+ Build-issue reported here: https://github.com/mateidavid/nanocall/issues/9
+
+ -- Andreas Tille <tille at debian.org> Tue, 13 Sep 2016 14:28:24 +0200
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..7bcd632
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,42 @@
+Source: nanocall
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cmake,
+ libfast5-dev,
+ libtclap-dev,
+ libhdf5-serial-dev,
+ zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/nanocall.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/nanocall.git
+Homepage: https://github.com/mateidavid/nanocall
+
+Package: nanocall
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: Basecaller for Oxford Nanopore Sequencing Data
+ The highly portable Oxford Nanopore MinION sequencer has enabled new
+ applications of genome sequencing directly in the field. However, the
+ MinION currently relies on a cloud computing platform, Metrichor
+ (metrichor.com), for translating locally generated sequencing data into
+ basecalls.
+ .
+ Nanocall allows offline and private analysis of MinION data. Nanocall is
+ the first freely-available, open-source basecaller for Oxford Nanopore
+ sequencing data and does not require an internet connection. Using R7.3
+ chemistry, on two E.coli and two human samples, with natural as well as
+ PCR-amplified DNA, Nanocall reads have ~68% identity, directly
+ comparable to Metrichor "1D" data. Further, Nanocall is efficient,
+ processing ~2500Kbp of sequence per core hour using the fastest
+ settings, and fully parallelized. Using a 4 core desktop computer,
+ Nanocall could basecall a MinION sequencing run in real time. Metrichor
+ provides the ability to integrate the "1D" sequencing of template and
+ complement strands of a single DNA molecule, and create a "2D" read.
+ Nanocall does not currently integrate this technology, and addition of
+ this capability will be an important future development. In summary,
+ Nanocall is the first open-source, freely available, off-line basecaller
+ for Oxford Nanopore sequencing data.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..1fc66a2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,51 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: nanocall
+Upstream-Contact: Matei David <matei.david at oicr.on.ca>
+Source: https://github.com/mateidavid/nanocall/releases
+
+Files: *
+Copyright: 2015-2016 Matei David <matei.david at oicr.on.ca>,
+ Jared Simpson,
+ Ontario Institute for Cancer Research
+License: expat
+License: expat
+ 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.
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: expat
+
+License: expat
+ 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/patches/remove_broken_makefile.patch b/debian/patches/remove_broken_makefile.patch
new file mode 100644
index 0000000..778a89f
--- /dev/null
+++ b/debian/patches/remove_broken_makefile.patch
@@ -0,0 +1,42 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 13 Sep 2016 14:28:24 +0200
+Description: Delete Makefile which does more harm than good - try cmake instead
+
+--- a/src/Makefile
++++ /dev/null
+@@ -1,35 +0,0 @@
+-SHELL := /bin/bash
+-
+-HDF_ROOT = /usr
+-
+-OPT_FLAG = -O0
+-CXXFLAGS = -Wall -Wextra -pedantic -g3 -ggdb -fno-eliminate-unused-debug-types ${OPT_FLAG}
+-M_CXXFLAGS = -std=c++11 -pthread
+-CPPFLAGS = -isystem ${HDF_ROOT}/include -I fast5/src -I tclap/include -I hpptools/include
+-
+-TARGETS = compute-state-transitions compute-scaled-pore-model run-fwbw run-viterbi nanocall
+-
+-.PHONY: all test clean
+-
+-all: ${TARGETS}
+-
+-clean:
+- rm -rf ${TARGETS}
+-
+-compute-state-transitions: compute-state-transitions.cpp
+- ${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS}
+-
+-compute-scaled-pore-model: compute-scaled-pore-model.cpp
+- ${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -L ${HDF_ROOT}/lib -lhdf5
+-
+-run-fwbw: run-fwbw.cpp
+- ${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -lz
+-
+-run-viterbi: run-viterbi.cpp
+- ${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -lz
+-
+-nanocall: nanocall.cpp Builtin_Model.cpp
+- ${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS} -L ${HDF_ROOT}/lib -lhdf5 -lz
+-
+-list-directory: list-directory.cpp
+- ${CXX} ${M_CXXFLAGS} ${CXXFLAGS} ${CPPFLAGS} $^ -o $@ ${LDFLAGS}
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..5b1926d
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+remove_broken_makefile.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..ad618bb
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@ --sourcedirectory=src
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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..5b3bae7
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,9 @@
+Reference:
+ Author: Matei David and Lewis Jonathan Dursi and Delia Yao and Paul C Boutros and Jared T Simpson
+ Title: "Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data¨
+ Journal: Bioinformatics
+ Year: 2016
+ DOI: 10.1093/bioinformatics/btw569
+ PMID: 27614348
+ URL: http://bioinformatics.oxfordjournals.org/content/early/2016/09/07/bioinformatics.btw569
+ eprint: http://bioinformatics.oxfordjournals.org/content/early/2016/09/07/bioinformatics.btw569.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..95adcb2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/mateidavid/nanocall/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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