[med-svn] [miniasm] 01/03: add debian dir
Sascha Steinbiss
sascha at steinbiss.name
Sat Jan 23 22:16:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository miniasm.
commit 9136d6547b2be515c489438c536d524e7e654909
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sat Jan 23 13:42:39 2016 +0000
add debian dir
---
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 26 ++++++++++++++++++++
debian/copyright | 50 +++++++++++++++++++++++++++++++++++++++
debian/install | 1 +
debian/manpages | 1 +
debian/patches/ensure_64bit_value | 24 +++++++++++++++++++
debian/patches/hardening | 32 +++++++++++++++++++++++++
debian/patches/series | 2 ++
debian/rules | 4 ++++
debian/source/format | 1 +
debian/upstream/metadata | 8 +++++++
debian/watch | 3 +++
13 files changed, 158 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..73db205
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+miniasm (0.2-1) unstable; urgency=low
+
+ * Initial packaging (Closes: #NNNNNNNN)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 10 Jan 2016 11:34:09 +0000
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..6a8ab87
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,26 @@
+Source: miniasm
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ zlib1g-dev
+Standards-Version: 3.9.6
+Testsuite: autopkgtest
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/miniasm.git
+Vcs-Git: git://anonscm.debian.org/debian-med/miniasm.git
+Homepage: https://github.com/lh3/miniasm
+
+Package: miniasm
+Architecture: any
+Recommends: minimap
+Depends: ${misc:Depends},
+ ${shlibs:Depends},
+ zlib1g
+Description: ultrafast de novo assembler for long noisy DNA sequencing reads
+ Miniasm is an experimental very fast OLC-based de novo assembler for noisy
+ long reads. It takes all-vs-all read self-mappings (typically by minimap)
+ as input and outputs an assembly graph in the GFA format. Different from
+ mainstream assemblers, miniasm does not have a consensus step. It simply
+ concatenates pieces of read sequences to generate the final unitig sequences.
+ Thus the per-base error rate is similar to the raw input reads.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d51d906
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,50 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: minimap
+Source: https://github.com/lh3/minimap
+
+Files: *
+Copyright: © 2015 Broad Institute <hengli at broadinstitute.org>
+License: MIT
+
+Files: debian/*
+Copyright: © 2015 Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+License: GPL-3+
+
+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.
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..ac62007
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+miniasm /usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..e99c42a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+miniasm.1
diff --git a/debian/patches/ensure_64bit_value b/debian/patches/ensure_64bit_value
new file mode 100644
index 0000000..1e59686
--- /dev/null
+++ b/debian/patches/ensure_64bit_value
@@ -0,0 +1,24 @@
+Description: ensure 64 bit value
+ The bitfield requires 64 bits to be distributed, but size_t can
+ be less wide on some architectures.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+Forwarded: https://github.com/lh3/minimap/pull/2
+Applied-Upstream: https://github.com/lh3/minimap/commit/1cd6ae3bc7c7a6f9e7c03c0b7a93a12647bba244
+Last-Update: 2016-01-14
+--- a/kdq.h
++++ b/kdq.h
+@@ -1,12 +1,13 @@
+ #ifndef __AC_KDQ_H
+ #define __AC_KDQ_H
+
++#include <stdint.h>
+ #include <stdlib.h>
+ #include <string.h>
+
+ #define __KDQ_TYPE(type) \
+ typedef struct { \
+- size_t front:58, bits:6, count, mask; \
++ uint64_t front:58, bits:6, count, mask; \
+ type *a; \
+ } kdq_##type##_t;
+
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 0000000..7e5e267
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,32 @@
+Description: add hardening flags
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+Last-Update: 2016-01-14
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,5 @@
+ CC= gcc
+-CFLAGS= -g -Wall -O2 -Wc++-compat -Wno-unused-function
+-CPPFLAGS=
++CFLAGS+= -g -Wall -O2 -Wc++-compat -Wno-unused-function
+ INCLUDES= -I.
+ OBJS= sys.o sdict.o paf.o asg.o common.o hit.o asm.o
+ PROG= miniasm minidot
+@@ -9,15 +8,15 @@
+ .SUFFIXES:.c .o
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
++ $(CC) -c $(CFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ all:$(PROG)
+
+ miniasm:$(OBJS) main.o
+- $(CC) $(CFLAGS) $^ -o $@ $(LIBS)
++ $(CC) $(CXXFLAGS) $(CFLAGS) $^ -o $@ $(LIBS) $(LDFLAGS)
+
+ minidot:paf.o sdict.o dotter.o
+- $(CC) $(CFLAGS) $^ -o $@ $(LIBS)
++ $(CC) $(CXXFLAGS) $(CFLAGS) $^ -o $@ $(LIBS) $(LDFLAGS)
+
+ clean:
+ rm -fr gmon.out *.o a.out $(PROG) *~ *.a *.dSYM session*
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c1b77b3
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+ensure_64bit_value
+hardening
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..2d33f6a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+%:
+ 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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..800083e
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,8 @@
+Reference:
+ Author: Heng Li
+ Title: "Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences"
+ Journal: arXiv
+ Year: 2015
+ Pages: 1512.01801
+ URL: http://arxiv.org/abs/1512.01801
+ eprint: http://arxiv.org/pdf/1512.01801v1.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..f7580d3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+https://github.com/lh3/miniasm/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
--
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