[med-svn] [dazzdb] 02/02: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Sep 13 23:46:52 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository dazzdb.
commit f8c529db47e12638d7ecd1761d3c23728cde0037
Author: Afif Elghraoui <afif at 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 <afif at 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-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/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.myers at gmail.com>
+Source: http://github.com/PacificBiosciences/DAZZ_DB
+
+Files: *
+Copyright: 2013-2015 Eugene W. Myers <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/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 <afif at 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 <afif at 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 <afif at 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
--
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