[med-svn] [soapaligner] 01/10: Move to standard conform directory layout
Andreas Tille
tille at debian.org
Thu Dec 28 07:09:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository soapaligner.
commit 66794b598869452256b133d3841b0cdef6984525
Author: Andreas Tille <tille at debian.org>
Date: Fri Jun 8 10:05:52 2012 +0000
Move to standard conform directory layout
---
debian/README.Debian | 6 ++++
debian/README.source | 5 ++++
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 34 +++++++++++++++++++++
debian/copyright | 56 +++++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/genomics.cn-soap2.install | 1 +
debian/genomics.cn-soap2.manpages | 1 +
debian/patches/compiler_options.patch | 22 ++++++++++++++
debian/patches/series | 1 +
debian/rules | 8 +++++
debian/source/format | 1 +
debian/upstream | 14 +++++++++
debian/watch.ex | 23 ++++++++++++++
15 files changed, 179 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..82796e0
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,6 @@
+soap2 for Debian
+----------------
+
+The authors of this package demand the amd64 platform.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 21 Apr 2012 22:45:08 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..be7a7b5
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,5 @@
+soap2 for Debian
+----------------
+
+Only -O2 compilation is performed to keep maximal compatibility across platforms. The patch changes the Makefile accordingly.
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..aba1e40
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+genomics.cn-soap2 (2.20-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #669917)
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 21 Apr 2012 22:45:08 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..3384ac0
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,34 @@
+Source: genomics.cn-soap2
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/soap/soap2/trunk
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soap2/trunk
+Homepage: http://soap.genomics.org.cn/soapaligner.html
+
+Package: genomics.cn-soap2
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: aligner of short reads of next generation sequencers
+ This package addresses a common problem in bioinformatics that has
+ become routine now also in clinical research: the assembly and
+ comparison of the very long genomic DNA sequences from many
+ short reads that the machines provide.
+ .
+ SOAPaligner/soap2 is a member of the Short Oligonucleotide Analysis
+ Package (SOAP) and an updated version of SOAP software for short
+ oligonucleotide alignment (soap v1). The new program features in super
+ fast and accurate alignment for huge amounts of short reads generated by
+ Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order
+ of magnitude faster. It require only 2 minutes aligning one million
+ single-end reads onto the human reference genome. Another remarkable
+ improvement of SOAPaligner is that it now supports a wide range of the
+ read length.
+ .
+ SOAPaligner/soap2 benefitted in time and space efficiency by a revolution
+ in the basic data structures and algorithms used. The core algorithms and
+ the indexing data structures (2way-BWT) are developed by the algorithms
+ research group of the Department of Computer Science, the University
+ of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..df2efd4
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,56 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: soap2
+Source: http://soap.genomics.org.cn/soapaligner.html
+
+Files: *
+Copyright: 2004 Wong Chi Kwong
+ 2009 BGI Shenzhen, Chang Yu <yuchang at genomics.org.cn>
+License: GPL-3.0+
+
+Files: stdaln.c
+Copyright: 2003-2006, 2008 Heng Li <lh3lh3 at gmail.com>
+License: MIT
+
+Files: debian/*
+Copyright: 2012 Steffen Moeller <moeller at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program 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".
+
+
+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.
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..edc0071
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+NEWS
diff --git a/debian/genomics.cn-soap2.install b/debian/genomics.cn-soap2.install
new file mode 100644
index 0000000..ad6f5cc
--- /dev/null
+++ b/debian/genomics.cn-soap2.install
@@ -0,0 +1 @@
+soap usr/bin
diff --git a/debian/genomics.cn-soap2.manpages b/debian/genomics.cn-soap2.manpages
new file mode 100644
index 0000000..e6b9541
--- /dev/null
+++ b/debian/genomics.cn-soap2.manpages
@@ -0,0 +1 @@
+soap.1
diff --git a/debian/patches/compiler_options.patch b/debian/patches/compiler_options.patch
new file mode 100644
index 0000000..fc02902
--- /dev/null
+++ b/debian/patches/compiler_options.patch
@@ -0,0 +1,22 @@
+Index: soap2-2.20/Makefile
+===================================================================
+--- soap2-2.20.orig/Makefile 2009-07-23 00:49:31.000000000 +0200
++++ soap2-2.20/Makefile 2012-04-22 00:01:01.446041368 +0200
+@@ -6,7 +6,7 @@
+ CC = gcc
+ DEBUG_FLAGS = -g3 -Wall -O2
+ PROFILE_FLAGS = -fprofile-arcs -ftest-coverage -pg
+-RELEASE_FLAGS = -msse3 -O3 -static -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
++RELEASE_FLAGS = $(DEBUG_FLAGS)
+ STATIC_FLAGS = -static
+ DFLAGS = -DMAKE_TIME=\""`date`"\"
+ LIBS = -lm
+@@ -18,7 +18,7 @@
+ DFLAGS += -DDEBUG
+ # PTHREADS = NO
+ else
+- CFLAGS = $(RELEASE_FLAGS) $(STATIC_FLAGS)
++ CFLAGS = $(RELEASE_FLAGS)
+ endif
+
+ ifeq (YES, $(PTHREADS))
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..a122bcc
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+compiler_options.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..79fd842
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ 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 b/debian/upstream
new file mode 100644
index 0000000..ecbbfa2
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,14 @@
+Contact: soap at genomics.org.cn
+Homepage: http://soap.genomics.org.cn/soapaligner.html
+Reference:
+ DOI: 10.1093/bioinformatics/btn025
+ Eprint: http://bioinformatics.oxfordjournals.org/content/24/5/713.full.pdf+html
+ Journal: Genome Res.
+ PMID: 18227114
+ Author: Ruiqiang Li and Yingrui Li and Karsten Kristiansen and Jun Wang
+ Title: "SOAP: short oligonucleotide alignment program"
+ URL: http://bioinformatics.oxfordjournals.org/content/24/5/713.full
+ Volume: 24
+ Number: 5
+ Pages: 713-714
+ Year: 2008
diff --git a/debian/watch.ex b/debian/watch.ex
new file mode 100644
index 0000000..e5af267
--- /dev/null
+++ b/debian/watch.ex
@@ -0,0 +1,23 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php soap2-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/soap2-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/soap2-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for devscripts >= 2.9
+# http://sf.net/soap2/soap2-(.*)\.tar\.gz
+
+# Uncomment to find new files on GooglePages
+# http://example.googlepages.com/foo.html soap2-(.*)\.tar\.gz
--
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