debian/0000755000000000000000000000000012117350771007172 5ustar debian/ltrsift.menu0000644000000000000000000000035312116606120011537 0ustar ?package(ltrsift): needs="X11" \ section="Applications/Science/Biology" \ title="LTRsift" \ command="/usr/bin/ltrsift" \ icon="/usr/share/pixmaps/ltrsift.xpm" debian/man-src/0000755000000000000000000000000012117350675010535 5ustar debian/man-src/ltrsift_encode.1.txt0000644000000000000000000000056012116606120014426 0ustar LTRSIFT-ENCODE(1) ================= NAME ---- ltrsift_encode - encode sequences into a LTRsift-compatible format SYNOPSIS -------- ltrsift_encode DESCRIPTION ----------- This command creates an index with name from the FASTA/EMBL/GenBank file . AUTHOR ------ Report bugs to . debian/man-src/ltrsift.1.txt0000644000000000000000000000174312116606120013115 0ustar LTRSIFT(1) ========== NAME ---- ltrsift - a graphical interface for postprocessing and classification of LTR retrotransposon candidates SYNOPSIS -------- ltrsift DESCRIPTION ----------- 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. CONFIGURATION ------------- The LAST binaries (lastal and lastdb) should be located in the system search path. If they are not, is it possible to specify their location using the ``GT_LAST_PATH" environment variable prior to running LTRsift. The same applies for the BLAST location. Use ``GT_BLAST_PATH'' to specify the the full path to the ``blastall'' executable. Style files (describing how the linear diagram of the candidate features look like) can be set via the LTRSIFT_STYLE_FILE environment variable. A sensible default style is built into LTRsift. AUTHOR ------ Report bugs to . debian/copyright0000644000000000000000000000352012116606120011114 0ustar Format: http://dep.debian.net/deps/dep5 Upstream-Name: ltrsift Source: http://www.zbh.uni-hamburg.de/LTRsift Files: * Copyright: 2012 Sascha Steinbiss 2012 Sascha Kastens 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 . 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 2012 Center for Bioinformatics, University of Hamburg License: 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. debian/upstream0000644000000000000000000000171412116606120010747 0ustar Name: LTRsift Bug-Database: http://ltrsift.lighthouseapp.com/projects/98871-ltrsift/tickets?q=all Bug-Submit: http://ltrsift.lighthouseapp.com/projects/98871-ltrsift/tickets/new Contact: Sascha Steinbiss Homepage: http://www.zbh.uni-hamburg.de/LTRsift Reference: Author: Steinbiss, Sascha and Kastens, Sascha and Kurtz, Stefan Title: > LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Journal: Mobile DNA Year: 2012 Volume: 3 Number: 1 Pages: 18 DOI: 10.1186/1759-8753-3-18 PMID: 23131050 URL: http://www.mobilednajournal.com/content/3/1/18/abstract eprint: http://www.mobilednajournal.com/content/pdf/1759-8753-3-18.pdf Repository: http://github.com/satta/ltrsift Screenshots: http://www.zbh.uni-hamburg.de/en/research/genome-informatics/software/ltrsift.html Watch: | https://github.com/satta/ltrsift/tags .*/zipball/v(\d[\d\.]+) debian/compat0000644000000000000000000000000212116606120010357 0ustar 9 debian/dirs0000644000000000000000000000014312116606120010043 0ustar /usr/share/pixmaps /usr/share/applications usr/share/icons/hicolor/scalable/apps usr/share/ltrsift debian/rules0000755000000000000000000000130112116606120010234 0ustar #!/usr/bin/make -f # -*- makefile -*- #export DH_VERBOSE=1 export DESTDIR=$(CURDIR)/debian/tmp export gt_prefix=/usr BITS:=$(shell dpkg-architecture | grep DEB_BUILD_ARCH_BITS | cut -f 2 -d'=') ifeq ($(BITS),64) 64BIT:=yes else 64BIT:=no endif %: dh $@ --parallel override_dh_auto_clean: $(MAKE) cleanup override_dh_auto_build: dh_auto_build --parallel -- 64bit=$(64BIT) errorcheck=no override_dh_auto_test: #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5 override_dh_auto_install: dh_auto_install -- 64bit=$(64BIT) errorcheck=no prefix=$(DESTDIR)/usr override_dh_strip: dh_strip --dbg-package=ltrsift-dbg override_dh_installdocs: dh_installdocs --exclude=license.template debian/ltrsift-examples.examples0000644000000000000000000000022312116606120014221 0ustar 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 debian/ltrsift.desktop0000644000000000000000000000035212116606120012243 0ustar [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 debian/control0000644000000000000000000000416212116606120010567 0ustar Source: ltrsift Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Build-Depends: debhelper (>= 9), libgenometools0-dev (>= 1.4.2), libgtk2.0-dev, libglib2.0-dev Standards-Version: 3.9.4 Homepage: http://www.zbh.uni-hamburg.de/LTRsift Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/ltrsift/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ltrsift/trunk/ Package: ltrsift Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2), 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 Depends: ${shlibs:Depends}, ${misc:Depends}, ltrsift (= ${binary:Version}) Section: debug Priority: extra 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. debian/ltrsift.manpages0000644000000000000000000000001512116606120012361 0ustar debian/man/* debian/ltrsift.docs0000644000000000000000000000001712116606120011520 0ustar README VERSION debian/changelog0000644000000000000000000000074512117350244011045 0ustar ltrsift (1.0.2-1) unstable; urgency=low * New upstream release -- Sascha Steinbiss Mon, 11 Mar 2013 13:39:05 +0100 ltrsift (1.0.1-2) unstable; urgency=low * enable optimization and hardening -- Sascha Steinbiss Sat, 09 Mar 2013 11:23:10 +0100 ltrsift (1.0.1-1) unstable; urgency=low * Initial release (Closes: #689961) -- Sascha Steinbiss Sun, 06 Oct 2012 15:08:11 +0200 debian/ltrsift.install0000644000000000000000000000032412116606120012237 0ustar 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 debian/man/0000755000000000000000000000000012117350675007750 5ustar debian/man/ltrsift.10000644000000000000000000000417312116606120011512 0ustar '\" t .\" Title: ltrsift .\" Author: [see the "AUTHOR" section] .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 10/07/2012 .\" Manual: \ \& .\" Source: \ \& .\" Language: English .\" .TH "LTRSIFT" "1" "10/07/2012" "\ \&" "\ \&" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ltrsift \- a graphical interface for postprocessing and classification of LTR retrotransposon candidates .SH "SYNOPSIS" .sp ltrsift .SH "DESCRIPTION" .sp 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\&. .SH "CONFIGURATION" .sp The LAST binaries (lastal and lastdb) should be located in the system search path\&. If they are not, is it possible to specify their location using the \(lqGT_LAST_PATH" environment variable prior to running LTRsift\&. The same applies for the BLAST location\&. Use ``GT_BLAST_PATH\(rq to specify the the full path to the \(lqblastall\(rq executable\&. .sp Style files (describing how the linear diagram of the candidate features look like) can be set via the LTRSIFT_STYLE_FILE environment variable\&. A sensible default style is built into LTRsift\&. .SH "AUTHOR" .sp Report bugs to \&. debian/man/ltrsift_encode.10000644000000000000000000000277012116606120013030 0ustar '\" t .\" Title: ltrsift-encode .\" Author: [see the "AUTHOR" section] .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 10/07/2012 .\" Manual: \ \& .\" Source: \ \& .\" Language: English .\" .TH "LTRSIFT\-ENCODE" "1" "10/07/2012" "\ \&" "\ \&" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ltrsift_encode \- encode sequences into a LTRsift\-compatible format .SH "SYNOPSIS" .sp ltrsift_encode .SH "DESCRIPTION" .sp This command creates an index with name from the FASTA/EMBL/GenBank file \&. .SH "AUTHOR" .sp Report bugs to \&. debian/ltrsift.svg0000644000000000000000000004643712116606120011407 0ustar image/svg+xml document search find Lapo Calamandrei Jakub Steiner 2006-04-21 debian/watch0000644000000000000000000000044512116606120010215 0ustar 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 Sat, 22 Dec 2012 13:05:45 +0000 debian/source/0000755000000000000000000000000012117350675010475 5ustar debian/source/format0000644000000000000000000000001412116606120011667 0ustar 3.0 (quilt) debian/ltrsift.xpm0000644000000000000000000001250712116606120011403 0ustar /* XPM */ static char * ltrsift_xpm[] = { "32 32 201 2", " c None", ". c #00C9F8", "+ c #08C8F6", "@ c #86C5CF", "# c #B1C5C3", "$ c #BEC8C4", "% c #CCD0CA", "& c #D7D9D4", "* c #CCD0CB", "= c #BFC8C3", "- c #B1C4C2", "; c #8BC4CD", "> c #0CC8F5", ", c #00C8F7", "' c #00C8F8", ") c #3AC6E6", "! 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