[med-svn] [sprai] 02/02: Initial packaging
Afif Elghraoui
afif at moszumanska.debian.org
Wed Apr 13 07:08:57 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository sprai.
commit 3e2e257ba2045e82b489e7954197d8255fb39ac9
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Tue Apr 12 23:41:06 2016 -0700
Initial packaging
---
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 31 +++++++++++++++++++++++++
debian/copyright | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++++
debian/docs | 3 +++
debian/examples | 3 +++
debian/repack-waf | 48 ++++++++++++++++++++++++++++++++++++++
debian/rules | 22 ++++++++++++++++++
debian/source/format | 1 +
debian/watch | 10 ++++++++
10 files changed, 189 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..cf02bb2
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sprai (0.9.9.12+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #820851)
+
+ -- Afif Elghraoui <afif at debian.org> Sat, 24 Oct 2015 23:29:31 -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..9ceb697
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: sprai
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at debian.org>
+Build-Depends:
+ debhelper (>= 9),
+ python-all,
+ libstatistics-descriptive-perl,
+Standards-Version: 3.9.7
+Homepage: http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html
+Vcs-Git: https://anonscm.debian.org/git/debian-med/sprai.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sprai.git
+
+Package: sprai
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${perl:Depends},
+ libstatistics-descriptive-perl,
+ python,
+ ncbi-blast+ (>= 2.2.27),
+Description: single-pass sequencing read accuracy improver
+ Sprai is a tool to correct sequencing errors in single-pass reads for
+ de novo assembly. It is originally designed for correcting sequencing
+ errors in single-molecule DNA sequencing reads, especially in Continuous
+ Long Reads (CLRs) generated by PacBio RS sequencers. The goal of Sprai is
+ not maximizing the accuracy of error-corrected reads. Instead, Sprai aims
+ at maximizing the continuity (i.e., N50 contig length) of assembled contigs
+ after error correction.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d946d2e
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,65 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: sprai
+Upstream-Contact: Takamasa Imai <imai at cb.k.u-tokyo.ac.jp>
+Source: http://zombie.cb.k.u-tokyo.ac.jp/sprai/Download.html
+Files-Excluded:
+ doc/_build/html/*.html
+ doc/_build/html/*.js
+ doc/_build/html/*.inv
+ doc/_build/html/_static
+
+Files: *
+Copyright: 2013-2016 Takamasa Imai
+ Tomoaki Nishiyama
+ Masahiro Kasahara
+License: MIT
+
+Files: waf waflib/*
+Copyright: 2005-2012 Thomas Nagy
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2016 Afif Elghraoui <afif at debian.org>
+License: MIT
+
+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.
+
+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. The name of the author may not be used to endorse or promote products
+ derived from this software without specific prior written permission.
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "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 AUTHOR 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..3ce248d
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+doc/_build/html/_sources/README.txt
+doc/_build/html/_sources/FAQ.txt
+doc/_build/html/_sources/Contact.txt
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..4a1cc83
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,3 @@
+ec.spec
+pbasm.spec
+doc/_build/html/_sources/Example.txt
diff --git a/debian/repack-waf b/debian/repack-waf
new file mode 100755
index 0000000..485df96
--- /dev/null
+++ b/debian/repack-waf
@@ -0,0 +1,48 @@
+#!/bin/sh
+# Repack an upstream tarball, unpacking waf files inside it.
+#
+# Meant to be run by uscan(1) as the "command param", after repacking
+# (if any) by mk-origtargz. So you shouldn't give "repacksuffix" to
+# debian/watch; instead you should set it below; however this should
+# still match the dversionmangle in that file.
+#
+# This file was downloaded from
+# https://wiki.debian.org/UnpackWaf?action=AttachFile&do=view&target=repack-waf
+# and has been only slightly modified.
+
+repacksuffix="+dfsg"
+unwaf_paths=.
+
+# You shouldn't need to change anything below here.
+
+USAGE="Usage: $0 --upstream-version version filename"
+
+test "$1" = "--upstream-version" || { echo >&2 "$USAGE"; exit 2; }
+upstream="$2"
+filename="$3"
+
+source="$(dpkg-parsechangelog -SSource)"
+newups="${upstream}${repacksuffix}"
+basedir="$(dirname "$filename")"
+
+unpack_waf() {
+ local olddir="$PWD"
+ cd "$1"
+ test -x ./waf || return 1
+ ./waf --help > /dev/null
+ mv .waf-*/* .
+ sed -i '/^#==>$/,$d' waf
+ rmdir .waf-*
+ find waf* -name "*.pyc" -delete
+ cd "$olddir"
+}
+
+set -e
+
+tar -xf "$basedir/${source}_${upstream}.orig.tar.gz"
+cd "${source}-${upstream}"
+for i in $unwaf_paths; do unpack_waf "$i"; done
+cd ..
+mv "${source}-${upstream}" "${source}-${newups}"
+GZIP="-9fn" tar -czf "$basedir/${source}_${newups}.orig.tar.gz" "${source}-${newups}"
+rm -rf "${source}-${newups}"
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..2efdd45
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+#include /usr/share/dpkg/default.mk
+
+WAF = ./waf -vvv
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ $(WAF) configure --prefix=/usr
+
+override_dh_auto_build:
+ $(WAF) build
+
+override_dh_auto_install:
+ $(WAF) install --destdir=$(CURDIR)/debian/sprai
+
+override_dh_auto_clean:
+ $(WAF) distclean
+ find waflib -name "*.pyc" -delete
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..80d3c6f
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,10 @@
+version=3
+
+# No repacksuffix is specified because it's handled by debian/repack-waf.
+# See <https://wiki.debian.org/UnpackWaf>.
+opts="\
+ dversionmangle=s/\+dfsg\d?$//,\
+ repack,\
+" \
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/Download.html .*/sprai-(.*)\.tar\.gz \
+debian debian/repack-waf
--
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