[med-svn] r21726 - trunk/packages/ltrsift/trunk/debian
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Thu Apr 21 15:47:57 UTC 2016
Author: sascha-guest
Date: 2016-04-21 15:47:57 +0000 (Thu, 21 Apr 2016)
New Revision: 21726
Added:
trunk/packages/ltrsift/trunk/debian/README.status
Removed:
trunk/packages/ltrsift/trunk/debian/changelog
trunk/packages/ltrsift/trunk/debian/compat
trunk/packages/ltrsift/trunk/debian/control
trunk/packages/ltrsift/trunk/debian/copyright
trunk/packages/ltrsift/trunk/debian/dirs
trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples
trunk/packages/ltrsift/trunk/debian/ltrsift.desktop
trunk/packages/ltrsift/trunk/debian/ltrsift.docs
trunk/packages/ltrsift/trunk/debian/ltrsift.install
trunk/packages/ltrsift/trunk/debian/ltrsift.manpages
trunk/packages/ltrsift/trunk/debian/ltrsift.svg
trunk/packages/ltrsift/trunk/debian/ltrsift.xpm
trunk/packages/ltrsift/trunk/debian/man-src/
trunk/packages/ltrsift/trunk/debian/man/
trunk/packages/ltrsift/trunk/debian/patches/
trunk/packages/ltrsift/trunk/debian/rules
trunk/packages/ltrsift/trunk/debian/source/
trunk/packages/ltrsift/trunk/debian/upstream/
trunk/packages/ltrsift/trunk/debian/watch
Log:
document migration to Git
Added: trunk/packages/ltrsift/trunk/debian/README.status
===================================================================
--- trunk/packages/ltrsift/trunk/debian/README.status (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/README.status 2016-04-21 15:47:57 UTC (rev 21726)
@@ -0,0 +1 @@
+This package has been migrated to Git: https://anonscm.debian.org/git/debian-med/ltrsift.git
Deleted: trunk/packages/ltrsift/trunk/debian/changelog
===================================================================
--- trunk/packages/ltrsift/trunk/debian/changelog 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/changelog 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,45 +0,0 @@
-ltrsift (1.0.2-5) unstable; urgency=low
-
- * use deterministic file order for build
- * fix Metadata-Screenshots
- * fix build on x32
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 12 Dec 2015 09:38:35 +0000
-
-ltrsift (1.0.2-4) unstable; urgency=low
-
- * remove menu file
- * remove timestamp from example .gz
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 17 Oct 2015 15:24:49 +0000
-
-ltrsift (1.0.2-3) unstable; urgency=low
-
- * include patches
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Tue, 18 Nov 2014 20:12:45 +0000
-
-ltrsift (1.0.2-2) unstable; urgency=low
-
- * fix FTBFS on 64bit archs
- * lintian cleanups
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Tue, 18 Nov 2014 19:36:18 +0000
-
-ltrsift (1.0.2-1) unstable; urgency=low
-
- * New upstream release
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 11 Mar 2013 13:39:05 +0100
-
-ltrsift (1.0.1-2) unstable; urgency=low
-
- * enable optimization and hardening
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sat, 09 Mar 2013 11:23:10 +0100
-
-ltrsift (1.0.1-1) unstable; urgency=low
-
- * Initial release (Closes: #689961)
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sun, 06 Oct 2012 15:08:11 +0200
Deleted: trunk/packages/ltrsift/trunk/debian/compat
===================================================================
--- trunk/packages/ltrsift/trunk/debian/compat 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/compat 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1 +0,0 @@
-9
Deleted: trunk/packages/ltrsift/trunk/debian/control
===================================================================
--- trunk/packages/ltrsift/trunk/debian/control 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/control 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,54 +0,0 @@
-Source: ltrsift
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9),
- libgenometools0-dev,
- libgtk2.0-dev,
- libglib2.0-dev
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ltrsift/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ltrsift/trunk/
-Homepage: http://www.zbh.uni-hamburg.de/LTRsift
-
-Package: ltrsift
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- libgenometools0,
- libgtk2.0-0,
- libglib2.0-0
-Recommends: last-align,
- ncbi-blast+
-Description: postprocessing and classification of LTR retrotransposons
- LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
- novo predicted LTR retrotransposon annotations, such as the ones generated by
- LTRharvest and LTRdigest. Its user-friendly interface displays LTR
- retrotransposon candidates, their putative families and their internal
- structure in a hierarchical fashion, allowing the user to "sift" through the
- sometimes large results of de novo prediction software. It also offers
- customizable filtering and classification functionality.
-
-Package: ltrsift-dbg
-Architecture: any
-Section: debug
-Priority: extra
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ltrsift (= ${binary:Version})
-Description: postprocessing and classification of LTR retrotransposons, with debug symbols
- This package contains debug information stripped from LTRsift.
- You may decide to install it to help identifying issues, typically
- to help communication with upstream developers.
-
-Package: ltrsift-examples
-Architecture: all
-Depends: ${misc:Depends}
-Suggests: ltrsift
-Description: example data for LTRsift
- This package contains test sequences (gzipped FASTA) and annotations (GFF3)
- from the Drosophila melanogaster (fruit fly) genome, to be used in an example
- process of postprocessing and classification of newly detected LTR
- retrotransposons. Scripts for using LTRsift to encode the sequences into a
- format accepted by LTRsift are included as well.
Deleted: trunk/packages/ltrsift/trunk/debian/copyright
===================================================================
--- trunk/packages/ltrsift/trunk/debian/copyright 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/copyright 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,44 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: ltrsift
-Source: http://www.zbh.uni-hamburg.de/LTRsift
-
-Files:
- *
-Copyright:
- 2012 Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
- 2012 Sascha Kastens <mail at skastens.de>
-License: GPL-2+
- This package 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 2 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 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-Files:
- scripts/tar_root.sh
-Copyright:
- 2012 Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
- 2012 Center for Bioinformatics, University of Hamburg
-License: ISC
- Permission to use, copy, modify, and distribute this software for any
- purpose with or without fee is hereby granted, provided that the above
- copyright notice and this permission notice appear in all copies.
- .
- THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
- WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
- MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
- ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
- WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
- ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
- OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-
Deleted: trunk/packages/ltrsift/trunk/debian/dirs
===================================================================
--- trunk/packages/ltrsift/trunk/debian/dirs 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/dirs 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,4 +0,0 @@
-/usr/share/pixmaps
-/usr/share/applications
-usr/share/icons/hicolor/scalable/apps
-usr/share/ltrsift
Deleted: trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,5 +0,0 @@
-sample_data/clean_encseqs
-sample_data/prepare_encseqs
-sample_data/dmel58.ltrd.gff3
-sample_data/dmel-2L-chromosome-r5.8.fasta.gz
-sample_data/README
Deleted: trunk/packages/ltrsift/trunk/debian/ltrsift.desktop
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.desktop 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.desktop 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,10 +0,0 @@
-[Desktop Entry]
-Version=1.0
-Type=Application
-Terminal=false
-Exec=/usr/bin/ltrsift
-Name=LTRsift
-Comment=A graphical tool for postprocessing and classification of LTR retrotransposons.
-Categories=Biology;Science;Education;
-Icon=ltrsift
-Keywords=LTRsift;ltr;ltrsift;
Deleted: trunk/packages/ltrsift/trunk/debian/ltrsift.docs
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.docs 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.docs 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,2 +0,0 @@
-README
-VERSION
Deleted: trunk/packages/ltrsift/trunk/debian/ltrsift.install
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.install 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.install 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,6 +0,0 @@
-usr/bin/ltrsift
-usr/bin/ltrsift_encode
-usr/filters usr/share/ltrsift
-debian/ltrsift.desktop usr/share/applications
-debian/ltrsift.svg usr/share/icons/hicolor/scalable/apps
-debian/ltrsift.xpm usr/share/pixmaps
Deleted: trunk/packages/ltrsift/trunk/debian/ltrsift.manpages
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.manpages 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.manpages 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1 +0,0 @@
-debian/man/*
Deleted: trunk/packages/ltrsift/trunk/debian/ltrsift.svg
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.svg 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.svg 2016-04-21 15:47:57 UTC (rev 21726)
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- rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
- <dc:title></dc:title>
- <dc:subject>
- <rdf:Bag>
- <rdf:li>document</rdf:li>
- <rdf:li>search</rdf:li>
- <rdf:li>find</rdf:li>
- </rdf:Bag>
- </dc:subject>
- <cc:license
- rdf:resource="http://creativecommons.org/licenses/GPL/2.0/" />
- <dc:creator>
- <cc:Agent>
- <dc:title>Lapo Calamandrei</dc:title>
- </cc:Agent>
- </dc:creator>
- <dc:source />
- <dc:contributor>
- <cc:Agent>
- <dc:title>Jakub Steiner</dc:title>
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- </dc:contributor>
- <dc:date>2006-04-21</dc:date>
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- rdf:about="http://creativecommons.org/licenses/GPL/2.0/">
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Deleted: trunk/packages/ltrsift/trunk/debian/ltrsift.xpm
===================================================================
--- trunk/packages/ltrsift/trunk/debian/ltrsift.xpm 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.xpm 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,236 +0,0 @@
-/* XPM */
-static char * ltrsift_xpm[] = {
-"32 32 201 2",
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-". c #00C9F8",
-"+ c #08C8F6",
-"@ c #86C5CF",
-"# c #B1C5C3",
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-"% c #CCD0CA",
-"& c #D7D9D4",
-"* c #CCD0CB",
-"= c #BFC8C3",
-"- c #B1C4C2",
-"; c #8BC4CD",
-"> c #0CC8F5",
-", c #00C8F7",
-"' c #00C8F8",
-") c #3AC6E6",
-"! c #B5C5C3",
-"~ c #E0E2DF",
-"{ c #DEE0DC",
-"] c #C6C9C3",
-"^ c #B2B4AE",
-"/ c #9FA7A3",
-"( c #B1B4AE",
-"_ c #C5C8C2",
-": c #DBDCD8",
-"< c #DDDEDA",
-"[ c #B4C2C0",
-"} c #44C5E2",
-"| c #CBD0CB",
-"1 c #E4E6E3",
-"2 c #A6ADA8",
-"3 c #7CA3A8",
-"4 c #57B2C5",
-"5 c #27BCDF",
-"6 c #06C5F3",
-"7 c #25BDE1",
-"8 c #58B4C7",
-"9 c #7EA7AC",
-"0 c #A4ACA8",
-"a c #DEE0DB",
-"b c #C8CCC7",
-"c c #8EC0C7",
-"d c #01C8F8",
-"e c #8DC3CB",
-"f c #C8CAC5",
-"g c #939B97",
-"h c #5CAFBF",
-"i c #59B5CA",
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-"k c #C9CCC6",
-"l c #D4D5D1",
-"m c #97C0C4",
-"n c #C1C4BF",
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-"p c #969897",
-"q c #A0A2A2",
-"r c #C0C3BE",
-"s c #B6B9B8",
-"t c #E5E7E3",
-"u c #9EA09D",
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-"x c #B3B5B4",
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-" e & f g h i j k l m ",
-" n o p q & r ",
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-" y z A B C ",
-" D E F G H I ",
-" J J J K L M J J J J J J J J J J J J J J J N O P ",
-" Q J J J R S T J J J J J J J J J J J J J J J U V W J ",
-" Q J J J P X Y J J J J J J J J J J J J J J J Z ` .J ",
-" ..+. at . #.$.%. ",
-" &.&.&.*.=.-.;.&.&.&.&.&.&.&.&.&.&.&.&.&.>.,.'.). ",
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-" !.~.~.~.~.[.}.|.1.~.~.~.~.~.~.~.~.~.~.~.2.3.4.5.~.~. ",
-" 6.7.8.9. 0.a.b.c. ",
-" d.e.f.g. h.i.j.k.l.m. ",
-" n.o.p.y q.r.s.t.u.v.w.x.y.z.A.B.C. ",
-" D.E.F.G.H.w I.J.K.L.M. N.O.P.Q.R. ",
-" S.T.U.V.W. X.Y.Z.`. + ",
-" .+++ at +#+$+ ",
-" %+&+*+=+-+ ",
-" ;+>+,+'+ ",
-" )+!+ ",
-" "};
Deleted: trunk/packages/ltrsift/trunk/debian/rules
===================================================================
--- trunk/packages/ltrsift/trunk/debian/rules 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/rules 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,44 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-#export DH_VERBOSE=1
-export DESTDIR=$(CURDIR)/debian/tmp
-export gt_prefix=/usr
-
-DARCH:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH= | cut -f 2 -d'=')
-BITS:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH_BITS= | cut -f 2 -d'=')
-
-ifeq ($(DARCH),x32)
- X32:=yes
-else
- X32:=no
-endif
-
-ifeq ($(BITS),64)
- 64BIT:=yes
-else
- 64BIT:=no
-endif
-
-%:
- dh $@ --parallel
-
-override_dh_auto_clean:
- $(MAKE) cleanup
-
-override_dh_auto_build:
- dh_auto_build --parallel -- x32=$(X32) 64bit=$(64BIT) errorcheck=no
-
-override_dh_auto_test:
- #dh_auto_test -- useshared=yes x32=$(X32) 64bit=$(64BIT) testthreads=5
-
-override_dh_auto_install:
- gunzip sample_data/dmel-2L-chromosome-r5.8.fasta.gz
- gzip -n -9 sample_data/dmel-2L-chromosome-r5.8.fasta
- dh_auto_install -- 64bit=$(64BIT) errorcheck=no prefix=$(DESTDIR)/usr
-
-override_dh_strip:
- dh_strip --dbg-package=ltrsift-dbg
-
-override_dh_installdocs:
- dh_installdocs --exclude=license.template
Deleted: trunk/packages/ltrsift/trunk/debian/watch
===================================================================
--- trunk/packages/ltrsift/trunk/debian/watch 2016-04-19 12:59:46 UTC (rev 21725)
+++ trunk/packages/ltrsift/trunk/debian/watch 2016-04-21 15:47:57 UTC (rev 21726)
@@ -1,5 +0,0 @@
-version=3
-opts=uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha|b|a)\d*)$/$1~$2/,dversionmangle=s/\+(debian|dfsg|ds|deb)\d*$// \
-https://github.com/satta/ltrsift/tags .*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
-# Bart Martens <bartm at debian.org> Sat, 22 Dec 2012 13:05:45 +0000
-
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