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commit 3e2e257ba2045e82b489e7954197d8255fb39ac9 Author: Afif Elghraoui <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Afif Elghraoui <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sprai.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
