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commit f8c529db47e12638d7ecd1761d3c23728cde0037 Author: Afif Elghraoui <a...@ghraoui.name> Date: Sun Sep 13 16:46:37 2015 -0700 Initial packaging --- debian/changelog | 5 +++ debian/compat | 1 + debian/control | 41 ++++++++++++++++++++++++ debian/copyright | 37 ++++++++++++++++++++++ debian/docs | 1 + debian/patches/append-cflags | 12 +++++++ debian/patches/destdir | 17 ++++++++++ debian/patches/ldflags | 75 ++++++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 3 ++ debian/rules | 12 +++++++ debian/source/format | 1 + debian/watch | 4 +++ 12 files changed, 209 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..edbeeb0 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +dazzdb (1.0-1) UNRELEASED; urgency=low + + * Initial release (Closes: #798873) + + -- Afif Elghraoui <a...@ghraoui.name> Sat, 15 Aug 2015 21:29:42 -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..bb6a615 --- /dev/null +++ b/debian/control @@ -0,0 +1,41 @@ +Source: dazzdb +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/DAZZ_DB +Vcs-Git: git://anonscm.debian.org/git/debian-med/dazzdb.git +Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/dazzdb.git + +Package: dazzdb +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: manage nucleotide sequencing read data + To facilitate the multiple phases of the dazzler assembler, we organize all + the read data into what is effectively a database of the reads and their + meta-information. The design goals for this data base are as follows: + * The database stores the source Pacbio read information in such a way that + it can re-create the original input data, thus permitting a user to remove the + (effectively redundant) source files. This avoids duplicating the same data, + once in the source file and once in the database. + * The data base can be built up incrementally, that is new sequence data can + be added to the data base over time. + * The data base flexibly allows one to store any meta-data desired for reads. + This is accomplished with the concept of *tracks* that implementors can add as + they need them. + * The data is held in a compressed form equivalent to the .dexta and .dexqv + files of the data extraction module. Both the .fasta and .quiva information + for each read is held in the data base and can be recreated from it. + The .quiva information can be added separately and later on if desired. + * To facilitate job parallel, cluster operation of the phases of our + assembler, the database has a concept of a *current partitioning* in which + all the reads that are over a given length and optionally unique to a well, + are divided up into *blocks* containing roughly a given number of bases, + except possibly the last block which may have a short count. Often programs + con be run on blocks or pairs of blocks and each such job is reasonably well + balanced as the blocks are all the same size. One must be careful about + changing the partition during an assembly as doing so can void the structural + validity of any interim block-based results. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..337dd87 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,37 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: DAZZ_DB +Upstream-Contact: Eugene W. Myers <gene.my...@gmail.com> +Source: http://github.com/PacificBiosciences/DAZZ_DB + +Files: * +Copyright: 2013-2015 Eugene W. Myers <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/append-cflags b/debian/patches/append-cflags new file mode 100644 index 0000000..c3607c0 --- /dev/null +++ b/debian/patches/append-cflags @@ -0,0 +1,12 @@ +Description: Make upstream build system append to CFLAGS +Author: Afif Elghraoui <a...@ghraoui.name> +Forwarded: no +Last-Update: 2015-09-13 +--- dazzdb.orig/Makefile ++++ dazzdb/Makefile +@@ -1,4 +1,4 @@ +-CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing ++CFLAGS += -O3 -Wall -Wextra -fno-strict-aliasing + + ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow DBstats DBrm simulator \ + fasta2DAM DAM2fasta diff --git a/debian/patches/destdir b/debian/patches/destdir new file mode 100644 index 0000000..22fc2d8 --- /dev/null +++ b/debian/patches/destdir @@ -0,0 +1,17 @@ +Description: Set destination directory in upstream Makefile + Upstream's install target by default installs into ~/bin +Author: Afif Elghraoui <a...@ghraoui.name> +Forwarded: no +Last-Update: 2015-09-13 +--- dazzdb.orig/Makefile ++++ dazzdb/Makefile +@@ -60,7 +60,8 @@ + rm -f dazz.db.tar.gz + + install: +- cp $(ALL) ~/bin ++ install -d $(DESTDIR)/usr/bin ++ install $(ALL) $(DESTDIR)/usr/bin + + package: + make clean diff --git a/debian/patches/ldflags b/debian/patches/ldflags new file mode 100644 index 0000000..21a9723 --- /dev/null +++ b/debian/patches/ldflags @@ -0,0 +1,75 @@ +Description: Honor LDFLAGS in upstream Makefile +Author: Afif Elghraoui <a...@ghraoui.name> +Forwarded: no +Last-Update: 2015-09-13 +--- dazzdb.orig/Makefile ++++ dazzdb/Makefile +@@ -6,52 +6,52 @@ + all: $(ALL) + + fasta2DB: fasta2DB.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o fasta2DB fasta2DB.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o fasta2DB fasta2DB.c DB.c QV.c -lm $(LDFLAGS) + + DB2fasta: DB2fasta.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DB2fasta DB2fasta.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DB2fasta DB2fasta.c DB.c QV.c -lm $(LDFLAGS) + + quiva2DB: quiva2DB.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o quiva2DB quiva2DB.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o quiva2DB quiva2DB.c DB.c QV.c -lm $(LDFLAGS) + + DB2quiva: DB2quiva.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DB2quiva DB2quiva.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DB2quiva DB2quiva.c DB.c QV.c -lm $(LDFLAGS) + + DBsplit: DBsplit.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DBsplit DBsplit.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DBsplit DBsplit.c DB.c QV.c -lm $(LDFLAGS) + + DBdust: DBdust.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DBdust DBdust.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DBdust DBdust.c DB.c QV.c -lm $(LDFLAGS) + + Catrack: Catrack.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o Catrack Catrack.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o Catrack Catrack.c DB.c QV.c -lm $(LDFLAGS) + + DBshow: DBshow.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DBshow DBshow.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DBshow DBshow.c DB.c QV.c -lm $(LDFLAGS) + + DBstats: DBstats.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DBstats DBstats.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DBstats DBstats.c DB.c QV.c -lm $(LDFLAGS) + + DBrm: DBrm.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DBrm DBrm.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DBrm DBrm.c DB.c QV.c -lm $(LDFLAGS) + + simulator: simulator.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o simulator simulator.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o simulator simulator.c DB.c QV.c -lm $(LDFLAGS) + + fasta2DAM: fasta2DAM.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o fasta2DAM fasta2DAM.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o fasta2DAM fasta2DAM.c DB.c QV.c -lm $(LDFLAGS) + + DAM2fasta: DAM2fasta.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DAM2fasta DAM2fasta.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DAM2fasta DAM2fasta.c DB.c QV.c -lm $(LDFLAGS) + + DBupgrade.Sep.25.2014: DBupgrade.Sep.25.2014.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DBupgrade.Sep.25.2014 DBupgrade.Sep.25.2014.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DBupgrade.Sep.25.2014 DBupgrade.Sep.25.2014.c DB.c QV.c -lm $(LDFLAGS) + + DBupgrade.Dec.31.2014: DBupgrade.Dec.31.2014.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DBupgrade.Dec.31.2014 DBupgrade.Dec.31.2014.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DBupgrade.Dec.31.2014 DBupgrade.Dec.31.2014.c DB.c QV.c -lm $(LDFLAGS) + + DUSTupgrade.Jan.1.2015: DUSTupgrade.Jan.1.2015.c DB.c DB.h QV.c QV.h +- gcc $(CFLAGS) -o DUSTupgrade.Jan.1.2015 DUSTupgrade.Jan.1.2015.c DB.c QV.c -lm ++ gcc $(CFLAGS) -o DUSTupgrade.Jan.1.2015 DUSTupgrade.Jan.1.2015.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..51b1ec9 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,3 @@ +append-cflags +ldflags +destdir diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..c34329c --- /dev/null +++ b/debian/rules @@ -0,0 +1,12 @@ +#!/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 + +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) diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..5479e93 --- /dev/null +++ b/debian/watch @@ -0,0 +1,4 @@ +version=3 + +opts="filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/dazzdb-$1.tar.gz/" \ + https://github.com/thegenemyers/DAZZ_DB/tags (?:.*/)?[vV]?(\d[\d\.]*)\.tar\.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/dazzdb.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