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commit 09fd2d74d5c145d2c7d8e0fdf054532adfde76c0 Author: Afif Elghraoui <a...@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 <a...@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-packag...@lists.alioth.debian.org> +Uploaders: Afif Elghraoui <a...@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.my...@gmail.com> +Source: http://github.com/thegenemyers/DALIGNER + +Files: * +Copyright: 2013-2015 Eugene W. Myers, Jr. <gene.my...@gmail.com> +License: BSD-3-Clause + +Files: debian/* +Copyright: 2015 Afif Elghraoui <a...@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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/daligner.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit