debian/0000775000000000000000000000000012611611733007171 5ustar debian/source/0000775000000000000000000000000012472240050010464 5ustar debian/source/format0000664000000000000000000000001412472240050011672 0ustar 3.0 (quilt) debian/patches/0000775000000000000000000000000012472240050010613 5ustar debian/patches/fix-whatis0000664000000000000000000000077012472240050012625 0ustar --- a/TransDecoder.LongOrfs +++ b/TransDecoder.LongOrfs @@ -6,7 +6,7 @@ =head1 NAME -L - Transcriptome Protein Prediction +L - Transcriptome Protein Prediction =head1 USAGE --- a/TransDecoder.Predict +++ b/TransDecoder.Predict @@ -4,7 +4,7 @@ =head1 NAME -L - Transcriptome Protein Prediction +L - Transcriptome Protein Prediction =head1 USAGE debian/patches/cd-hit-est-rename0000664000000000000000000000047012472240050013745 0ustar --- transdecoder.orig/TransDecoder.Predict +++ transdecoder/TransDecoder.Predict @@ -56,7 +56,7 @@ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}"; -my ($cd_hit_est_exec) = &check_program('cd-hit-est'); +my ($cd_hit_est_exec) = &check_program('/usr/lib/cd-hit/cd-hit-est'); my ($transcripts_file,$train_file); debian/patches/series0000664000000000000000000000003512472240050012026 0ustar cd-hit-est-rename fix-whatis debian/transdecoder.install0000664000000000000000000000013512472240050013230 0ustar TransDecoder* /usr/lib/transdecoder PerlLib /usr/lib/transdecoder util /usr/lib/transdecoder debian/compat0000664000000000000000000000000212472240050010362 0ustar 9 debian/control0000664000000000000000000000537512472240050010601 0ustar Source: transdecoder Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Section: science Priority: optional Build-Depends: debhelper (>= 9), cd-hit, liburi-perl Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/transdecoder.git Vcs-Git: git://anonscm.debian.org/debian-med/transdecoder.git Homepage: https://transdecoder.github.io/ Package: transdecoder Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, cd-hit, liburi-perl Description: find coding regions within transcripts TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. . TransDecoder identifies likely coding sequences based on the following criteria: * a minimum length open reading frame (ORF) is found in a transcript sequence * a log-likelihood score similar to what is computed by the GeneID software is > 0. * the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames. * if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). * optional the putative peptide has a match to a Pfam domain above the noise cutoff score. Package: transdecoder-doc Architecture: all Section: doc Depends: ${misc:Depends}, ${perl:Depends} Description: find coding regions within transcripts TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. . TransDecoder identifies likely coding sequences based on the following criteria: * a minimum length open reading frame (ORF) is found in a transcript sequence * a log-likelihood score similar to what is computed by the GeneID software is > 0. * the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames. * if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). * optional the putative peptide has a match to a Pfam domain above the noise cutoff score. . This package contains the documentation and sample data. debian/watch0000664000000000000000000000026012472240050010213 0ustar version=3 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \ https://github.com/TransDecoder/Transdecoder/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) debian/transdecoder-doc.docs0000664000000000000000000000005412472240050013255 0ustar README debian/tests/run-tests Release.Notes debian/transdecoder.manpages0000664000000000000000000000001312472240050013350 0ustar debian/*.1 debian/transdecoder-doc.install0000664000000000000000000000004212472240050013770 0ustar sample_data /usr/lib/transdecoder debian/tests/0000775000000000000000000000000012472240050010326 5ustar debian/tests/control0000664000000000000000000000006712472240050011734 0ustar Tests: run-tests Depends: @ Restrictions: allow-stderr debian/tests/run-tests0000664000000000000000000000030012472240050012206 0ustar #!/bin/sh -e pkg=transdecoder if [ "$ADTTMP" = "" ] ; then ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` fi cd $ADTTMP cp -r /usr/lib/transdecoder . cd transdecoder/sample_data sh ./runMe.sh debian/changelog0000664000000000000000000000055112611611733011044 0ustar transdecoder (2.0.1+dfsg-1~ubuntu14.04.1) trusty-backports; urgency=medium * No-change backport to trusty (LP: #1506743) -- Micah Gersten Tue, 20 Oct 2015 23:26:03 -0500 transdecoder (2.0.1+dfsg-1) unstable; urgency=low * Initial release (Closes: #778300) -- Michael R. Crusoe Fri, 13 Feb 2015 06:26:24 -0500 debian/upstream/0000775000000000000000000000000012472240050011024 5ustar debian/upstream/metadata0000664000000000000000000000017012472240050012525 0ustar Reference: Author: Title: Journal: Year: Volume: Number: Pages: DOI: PMID: URL: eprint: debian/copyright0000664000000000000000000000350612472240050011123 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: TransDecoder Source: https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz Files-Excluded: transdecoder_plugins Files: * Copyright: (c) 2012, The Broad Institute, Inc. All rights reserved. License: BSD-3-clause Files: debian/* Copyright: © 2015, Michigan State University License: BSD-3-clause 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: . · Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . · 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. . · Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.** . THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE ''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 BROAD INSTITUTE 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. debian/transdecoder.links0000664000000000000000000000022512472240050012702 0ustar /usr/lib/transdecoder/TransDecoder.LongOrfs /usr/bin/TransDecoder.LongOrfs /usr/lib/transdecoder/TransDecoder.Predict /usr/bin/TransDecoder.Predict debian/rules0000775000000000000000000000172712472242724010265 0ustar #!/usr/bin/make -f DH_VERBOSE := 1 DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') %: dh $@ --parallel override_dh_auto_clean: cd ./sample_data && ./cleanme.pl override_dh_auto_build: override_dh_install: dh_install find debian/transdecoder -name '*.p?' | xargs sed -i \ 's=^#!/usr/local/bin/perl=#!/usr/bin/perl=' override_dh_installman: pod2man --section=1 --center="Transcriptome Protein Prediction" \ --release="$$VERSION" TransDecoder.LongOrfs > \ debian/TransDecoder.LongOrfs.1 pod2man --section=1 --center="Transcriptome Protein Prediction" \ --release="$$VERSION" TransDecoder.Predict > \ debian/TransDecoder.Predict.1 dh_installman get-orig-source: uscan --verbose --force-download --repack --compression xz override_dh_clean: # generated man pages dh_clean debian/TransDecoder.LongOrfs.1 debian/TransDecoder.Predict.1 debian/createmanpages0000775000000000000000000000075212472240050012075 0ustar #!/bin/sh MANDIR=debian mkdir -p $MANDIR VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` help2man --no-info --no-discard-stderr --help-option=" " \ --name='' \ --version-string="$VERSION" > $MANDIR/.1 cat <