[med-svn] [daligner] 02/02: Initial Packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Aug 16 04:24:40 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository daligner.
commit 09fd2d74d5c145d2c7d8e0fdf054532adfde76c0
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Aug 15 21:24:21 2015 -0700
Initial Packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 20 ++++++++++++++++++
debian/copyright | 37 +++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/patches/cflags | 8 +++++++
debian/patches/destdir-install | 12 +++++++++++
debian/patches/lddflags | 47 ++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 3 +++
debian/rules | 13 ++++++++++++
debian/source/format | 1 +
11 files changed, 148 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..dc74767
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+daligner (1.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sat, 15 Aug 2015 20:02:21 -0700
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..7fb8ea7
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,20 @@
+Source: daligner
+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)
+Standards-Version: 3.9.6
+Homepage: https://github.com/thegenemyers/DALIGNER
+Vcs-Git: git://anonscm.debian.org/debian-med/daligner.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/daligner.git
+
+Package: daligner
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: find all significant local alignments between nucleotide sequencing reads
+ These tools permit one to find all significant local alignments between
+ reads encoded in Dazzler database. The assumption is that the reads are
+ from a Pacific Biosciences RS II long read sequencer. That is, the reads
+ are long and noisy, up to 15% on average.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..9e4ab0b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,37 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: daligner
+Upstream-Contact: Eugene W. Myers, Jr. <gene.myers at gmail.com>
+Source: http://github.com/thegenemyers/DALIGNER
+
+Files: *
+Copyright: 2013-2015 Eugene W. Myers, Jr. <gene.myers at gmail.com>
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: BSD-3-Clause
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
+ 3. Neither the name of the copyright holders nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND 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 THE HOLDERS OR
+ 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..e845566
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README
diff --git a/debian/patches/cflags b/debian/patches/cflags
new file mode 100644
index 0000000..b207fc1
--- /dev/null
+++ b/debian/patches/cflags
@@ -0,0 +1,8 @@
+--- daligner.orig/Makefile
++++ daligner/Makefile
+@@ -1,4 +1,4 @@
+-CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing
++CFLAGS += -O3 -Wall -Wextra -fno-strict-aliasing
+
+ ALL = daligner HPCdaligner HPCmapper LAsort LAmerge LAsplit LAcat LAshow LAcheck
+
diff --git a/debian/patches/destdir-install b/debian/patches/destdir-install
new file mode 100644
index 0000000..4b283f5
--- /dev/null
+++ b/debian/patches/destdir-install
@@ -0,0 +1,12 @@
+--- daligner.orig/Makefile
++++ daligner/Makefile
+@@ -41,7 +41,8 @@
+ rm -f daligner.tar.gz
+
+ install:
+- cp $(ALL) ~/bin
++ install -d $(DESTDIR)/usr/bin
++ install $(ALL) $(DESTDIR)/usr/bin
+
+ package:
+ make clean
diff --git a/debian/patches/lddflags b/debian/patches/lddflags
new file mode 100644
index 0000000..2fd7038
--- /dev/null
+++ b/debian/patches/lddflags
@@ -0,0 +1,47 @@
+--- daligner.orig/Makefile
++++ daligner/Makefile
+@@ -5,34 +5,34 @@
+ all: $(ALL)
+
+ daligner: daligner.c filter.c filter.h align.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o daligner daligner.c filter.c align.c DB.c QV.c -lpthread -lm
++ gcc $(CFLAGS) -o daligner daligner.c filter.c align.c DB.c QV.c -lpthread -lm $(LDFLAGS)
+
+ HPCdaligner: HPCdaligner.c DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o HPCdaligner HPCdaligner.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o HPCdaligner HPCdaligner.c DB.c QV.c -lm $(LDFLAGS)
+
+ HPCmapper: HPCmapper.c DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o HPCmapper HPCmapper.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o HPCmapper HPCmapper.c DB.c QV.c -lm $(LDFLAGS)
+
+ LAsort: LAsort.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm $(LDFLAGS)
+
+ LAmerge: LAmerge.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm $(LDFLAGS)
+
+ LAshow: LAshow.c align.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm $(LDFLAGS)
+
+ LAcat: LAcat.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm $(LDFLAGS)
+
+ LAsplit: LAsplit.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm $(LDFLAGS)
+
+ LAcheck: LAcheck.c align.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm $(LDFLAGS)
+
+ LAupgrade.Dec.31.2014: LAupgrade.Dec.31.2014.c align.c align.h DB.c DB.h QV.c QV.h
+- gcc $(CFLAGS) -o LAupgrade.Dec.31.2014 LAupgrade.Dec.31.2014.c align.c DB.c QV.c -lm
++ gcc $(CFLAGS) -o LAupgrade.Dec.31.2014 LAupgrade.Dec.31.2014.c align.c DB.c QV.c -lm $(LDFLAGS)
+
+ clean:
+ rm -f $(ALL)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..8586f40
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+cflags
+lddflags
+destdir-install
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e8cd68b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+
+# output every command that modifies files on the build system.
+#DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# The upstream build system doesn't honor CPPFLAGS
+CFLAGS := $(CPPFLAGS) $(CFLAGS)
+
+%:
+ dh $@ --parallel
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)
--
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