debian/0000755000000000000000000000000012231765675007204 5ustar debian/upstream0000644000000000000000000000220112231765114010746 0ustar Contact: Cole Trapnell Homepage: http://cufflinks.cbcb.umd.edu/ Name: Cufflinks Reference: - Author: Cole Trapnell and Brian A Williams and Geo Pertea and Ali Mortazavi and Gordon Kwan and Marijke J van Baren and Steven L Salzberg and Barbara J Wold and Lior Pachter Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Journal: Nature Biotechnology DOI: doi:10.1038/nbt.1621 URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html Year: 2010 PMID: 20436464 Pages: 511-515 Volume: 28 Number: 5 Type: article - Author: "Cole Trapnell and Adam Roberts and Loyal Goff and Geo Pertea and Daehwan Kim and David R Kelley and Harold Pimentel and Steven L Salzberg and John L Rinn and Lior Pachter" Title: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Journal: Nat. Protocols Year: 2012 DOI: 10.1038/nprot.2012.016 URL: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html Pages: 562-578 Volume: 7 Number: 8 PMID: 22383036 Type: article debian/source/0000755000000000000000000000000012231765114010470 5ustar debian/source/format0000644000000000000000000000001412231765114011676 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000002117112231765114011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: tophat.cufflinks@gmail.com. Source: http://cufflinks.cbcb.umd.edu/downloads/cufflinks-1.3.0.tar.gz License: non-free Most of the source code of Cufflinks is under the Boost Software License version 1.0, with the exception of M4 macros under permissive licenses, and ‘locfit’, which contains an unfortunate non-free clause restricting benchmarks. . After compilation (in May 2012), Cufflinks was linked to Boost (BSL-1.0), the GNU libc (mostly LGPL-2.1+), the GNU libgcc and libstdc++ (GPL-3+ with version 3.1 of the GCC Runtime Library Exception), and the zlib (permissive license). . The python script cuffmerge is also under the BSL-1.0, and can be executed with Python without third-party libraries. Disclamer: This package is not part of the Debian operating system. The cufflinks source and binary Debian packages are part of the “non-free” area in our archive. The packages in this area are not part of the Debian system, although they have been configured for use with Debian. We nevertheless support the use of the cufflinks source and binary Debian packages and provide infrastructure for non-free packages (such as our bug tracking system and mailing lists). The licences of Cufflinks do not forbid Debian from using autobuilders to create binary packages. . The non-free component of Cufflinks is ‘locfit’ (see below). Files: * Copyright: Copyright (C) 2003-2010 Cole Trapnell et al © 2010 Adam Roberts © 2009 Geo Pertea © 2001 Vladimir Prus © 2001 Jeremy Siek © 2009 Eric Bose-Wolf License: BSL-1.0 Files: ax_bam.m4 Copyright: © 2010 Cole Trapnell License: GAP Files: ax_boost_base.m4 ax_boost_thread.m4 Copyright: © 2008,2009 Thomas Porschberg © 2009 Michael Tindal License: GAP Source: http://autoconf-archive.cryp.to/ Files: ax_check_zlib.m4 Copyright: © 2008 Loic Dachary License: GPL-2+_with_Autoconf_exception This program 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 program 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 . . As a special exception, the respective Autoconf Macro's copyright owner gives unlimited permission to copy, distribute and modify the configure scripts that are the output of Autoconf when processing the Macro. You need not follow the terms of the GNU General Public License when using or distributing such scripts, even though portions of the text of the Macro appear in them. The GNU General Public License (GPL) does govern all other use of the material that constitutes the Autoconf Macro. . This special exception to the GPL applies to versions of the Autoconf Macro released by the Autoconf Archive. When you make and distribute a modified version of the Autoconf Macro, you may extend this special exception to the GPL to apply to your modified version as well. Comment: On Debian systems, the full text of the GNU General Public license version 2 can be consulted in ‘/usr/share/common-licenses/GPL-2’. Source: http://www.gnu.org/software/autoconf-archive/ax_check_zlib.html Files: src/lemon/* Copyright: © 2003-2008 Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport (Egervary Research Group on Combinatorial Optimization, EGRES) © 2003 The Trustees of Indiana University © Jeremy Siek 2000 License: BSL-1.0 Comment: The files contain the following header: This file is a part of LEMON, a generic C++ optimization library . Copyright (C) 2003-2008 Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport (Egervary Research Group on Combinatorial Optimization, EGRES). . Permission to use, modify and distribute this software is granted provided that this copyright notice appears in all copies. For precise terms see the accompanying LICENSE file. . This software is provided "AS IS" with no warranty of any kind, express or implied, and with no claim as to its suitability for any purpose. . The license file at http://lemon.cs.elte.hu/trac/lemon/browser indicates the Boost Software License, Version 1.0. Source: http://lemon.cs.elte.hu/trac/lemon Files: src/locfit/* Copyright: © 1996-2001 Lucent Technologies, Bell Laboratories. © 1996-2001 Catherine Loader. License: Locfit ABOUT ALGORITHMS: The Locfit implementation has been designed largely from the point of view of generality: to provide a set of functions that can be used for as wide a range of local fitting problems as possible. It is not intended to be the fastest or most efficient implementation possible. In addition to generality, the code in many places makes extensive trade-offs made between speed and numerical accuracy (some of which can be controlled through optional arguments). Many of Locfit's options will only be used in a small fraction of cases; for other cases, they add to the cost of overhead (an obvious example is multi-dimensional fitting: when used in 1-d, many loops reduce to for(i=0;i<1;i++)). Additionally, the user interfaces (i.e. the R and S-Plus code) add significantly to the computational overhead. For these reasons, the Locfit code, as distributed, should not, and can not, be used to derive meaningful benchmarks, either for the speed or accuracy of algorithms. Anyone wishing to use Locfit in any kind of comparative benchmark study must contact and obtain permission from the Author. . COPYRIGHT: . Copyright (c) 1996-2001 Lucent Technologies, Bell Laboratories. SCB code is Copyright (c) 1996-2001 Jiayang Sun. . Permission to use, copy, modify, and distribute this software for any purpose (with the exceptions noted in `About Algorithms' above) without fee is hereby granted, and provided that this entire notice is included in all copies of any software which is or includes a copy or modification of this software and in all copies of the supporting documentation for such software. . THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. IN PARTICULAR, NEITHER THE AUTHOR NOR LUCENT TECHNOLOGIES MAKE ANY REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE. Comment: the files contain “See README file for details.” and the license displayed above is from the README file of the locfit source available at http://stat.bell-labs.com/project/locfit/dist/locfit.tgz Source: http://stat.bell-labs.com/project/locfit Files: debian/* Copyright: 2011 Alex Mestiashvili License: BSL-1.0 License: BSL-1.0 Boost Software License, Version 1.0 . Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: . The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. . 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, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. License: GAP Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. Comment: GAP stands for GNU All Permissive, see: http://www.gnu.org/s/hello/manual/texinfo/All_002dpermissive-Copying-License.html debian/cuffcompare.10000644000000000000000000000435612231765114011554 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4. .TH CUFFCOMPARE "1" "May 2011" "cuffcompare v1.0.2 (2335)" "User Commands" .SH NAME cuffcompare \- helps analyze the transfrags .SH SYNOPSIS cuffcompare [\-r ] [\-R] [\-T] [\-V] [\-s ] .IP [\-o ] [\-p ] {\-i | [ .. ]} .IP .SH DESCRIPTION Cuffcompare provides classification, reference annotation mapping and various statistics for Cufflinks transfrags. Cuffcompare clusters and tracks transfrags across multiple samples, writing matching transcripts (intron chains) into .tracking, and a GTF file .combined.gtf containing a nonredundant set of transcripts across all input files (with a single representative transfrag chosen for each clique of matching transfrags across samples). .SH OPTIONS \fB\-i\fR provide a text file with a list of Cufflinks GTF files to process instead .IP of expecting them as command line arguments (useful when a large number of GTF files should be processed) .PP \fB\-r\fR a set of known mRNAs to use as a reference for assessing .IP the accuracy of mRNAs or gene models given in .PP \fB\-R\fR for \fB\-r\fR option, reduce the set of reference transcripts to .IP only those found to overlap any of the input loci .PP \fB\-M\fR discard (ignore) single\-exon transfrags and reference transcripts \fB\-N\fR discard (ignore) single\-exon reference transcripts .PP \fB\-s\fR can be a multi\-fasta file with all the genomic sequences or .IP a directory containing multiple single\-fasta files (one file per contig); lower case bases will be used to classify input transcripts as repeats .PP \fB\-d\fR max distance (range) for grouping transcript start sites (100) \fB\-p\fR the name prefix to use for consensus transcripts in the .IP .combined.gtf file (default: 'TCONS') .PP \fB\-C\fR include the "contained" transcripts in the .combined.gtf file \fB\-G\fR generic GFF input file(s) (do not assume Cufflinks GTF) \fB\-T\fR do not generate .tmap and .refmap files for each input file \fB\-V\fR verbose processing mode (showing all GFF parsing warnings) .PP .SH SEE ALSO http://cufflinks.cbcb.umd.edu/manual.html#cuffcompare debian/cufflinks.manpages0000644000000000000000000000001312231765114012663 0ustar debian/*.1 debian/changelog0000644000000000000000000000741612231765656011065 0ustar cufflinks (2.1.1-4) unstable; urgency=low * Force use boost_system, boost_thread when linking. Fixing FTBFS in ubuntu. * Enable parallel build. -- Dmitrijs Ledkovs Wed, 23 Oct 2013 16:30:40 +0100 cufflinks (2.1.1-3) unstable; urgency=low * Rebuild against boost1.54. -- Dmitrijs Ledkovs Sat, 07 Sep 2013 17:10:26 +0100 cufflinks (2.1.1-2) unstable; urgency=low * Fix failing to build from source against boost1.53. (Closes: #709252) -- Dmitrijs Ledkovs Thu, 23 May 2013 01:05:02 +0100 cufflinks (2.1.1-1) unstable; urgency=low [Carlos Borroto] * New upstream release. * Added libeigen3-dev to build-deps. * Modified fix_includes_path to properly include Eigen library. * Bumped libboost-dev requirement to >= 1.47.0 [ Alexandre Mestiashvili ] * Imported debian/patches/0004-fix-m64-usage-and-lfs.patch, Closes: #675985 [ Andreas Tille ] * Upstream release 2.1.1 (+ adapted patches) Closes: #687968 * debian/control: - Removed: DM-Upload-Allowed - Standards-Version: 3.9.4 - Debhelper 9 (also d/compat) requires d/p/format-security.patch for hardening via --format-security - normalised format -- Andreas Tille Wed, 22 May 2013 13:27:40 +0200 cufflinks (1.3.0-2) unstable; urgency=low [ Charles Plessy ] * Normalised and summarised debian/copyright. [ Carlos Borroto ] * Added tophat to Enhances [ Andreas Tille ] * debian/upstream: Added references as specified in tasks file * debian/copyright: Added Upstream-Contact e-mail * debian/patches/gcc-4.7.patch: Fix gcc-4.7 build issue Closes: #672744 -- Charles Plessy Thu, 24 May 2012 12:36:16 +0900 cufflinks (1.3.0-1) unstable; urgency=low [ Alexandre Mestiashvili ] * New upstream release * Fixed spelling error. * Updated source version [ Charles Plessy ] * Removed quilt patch management, and rely on dpkg-dev exclusively. -- Charles Plessy Fri, 06 Jan 2012 09:20:23 +0900 cufflinks (1.2.1-1) unstable; urgency=low [ Alexandre Mestiashvili ] * New upstream release * added patch to fix bam.h location . * debian/rules invoke autoreconf * debian/rules added overrides for dh_auto_clean and dh_clean * added missing dependency - quilt .We use dh_quilt_patch, dh_quilt_unpatch helpers * debian/control added dependency python (>=2.6.6-3~) for source package * debian/control added dependency python (>=2.6.6-3~) for binary package [ Andreas Tille ] * Added myself to uploaders * Debhelper 8 (control+compat) * debian/watch: removed dh-make template from watch file * debian/rules: invoke autotools_dev [ Charles Plessy ] * Switch to non-free section because of the locfit license (debian/control). * Added myself to Uploaders (debian/control). * Compress binary package with xz (debian/rules). * Pre-depend on dpkg (>= 1.15.6) for xz compression (Ubuntu LTS). -- Charles Plessy Sun, 11 Dec 2011 12:07:02 +0900 cufflinks (1.0.3-1) UNRELEASED; urgency=low [ Alex Mestiashvili ] * added docs * added missing dependency * libbam-dev provides necessary headers only from 0.1.16 version . Fixed in control file. [ Charles Plessy ] * Add debian/gbp.conf to show the package is managed with git-buildpackage. * Converted Debian copyright file to machine-readable format (DEP 5). * Reviewed copyright and license notices, and found that locfit is non-free… [ Alex Mestiashvili ] * Imported Upstream version 1.0.3 (bugfix) -- Alex Mestiashvili Wed, 08 Jun 2011 06:31:10 +0000 cufflinks (1.0.2-1) UNRELEASED; urgency=low * Initial release (Closes: #627799) -- Alex Mestiashvili Tue, 24 May 2011 13:43:09 +0200 debian/gbp.conf0000644000000000000000000000015012231765114010603 0ustar # This source package is managed with git-buildpackage and pristine-tar. [DEFAULT] pristine-tar = True debian/control0000644000000000000000000000265412231765157010611 0ustar Source: cufflinks Maintainer: Debian Med Packaging Team Uploaders: Alexandre Mestiashvili , Andreas Tille , Charles Plessy Section: non-free/science Priority: optional Build-Depends: debhelper (>= 9), autotools-dev, libboost-dev (>=1.47.0), libboost-thread-dev (>=1.47.0), libboost-system-dev (>=1.47.0), libbam-dev (>=0.1.16), zlib1g-dev, dh-autoreconf, python (>=2.6.6-3~), libeigen3-dev Standards-Version: 3.9.4 Vcs-Git: git://git.debian.org/debian-med/cufflinks.git Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary Homepage: http://cufflinks.cbcb.umd.edu/ Package: cufflinks Architecture: any Pre-Depends: dpkg (>= 1.15.6) Depends: ${shlibs:Depends}, ${misc:Depends}, python (>=2.6.6-3~) Enhances: tophat Description: Transcript assembly, differential expression and regulation for RNA-Seq Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. debian/gffread.10000644000000000000000000001511212231765114010650 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4. .TH GFFREAD "1" "May 2011" "gffread Usage:" "User Commands" .SH NAME gffread \- one of the cufflinks tools .SH SYSNOPSIS gffread [\-g | ][\-s ] .IP [\-o ] [\-t ] [\-r [[]:]..] [\-CTVNMAFGRUVBHSZWTOE] [\-w ] [\-x ] [\-y ] [\-i ] Filters and/or converts GFF3/GTF2 records. is a GFF file, use '\-' if the GFF records will be given at stdin .IP .SH Options .TP \fB\-g\fR full path to a multi\-fasta file with the genomic sequences for all input mappings, OR a directory with single\-fasta files (one per genomic sequence, with file names matching sequence names) .TP \fB\-s\fR is a tab\-delimited file providing this info for each of the mapped sequences: (useful for mRNA/EST/protein mappings with \fB\-A\fR option) .TP \fB\-i\fR discard transcripts having an intron larger than .TP \fB\-r\fR only show transcripts crossing coordinate range .. (on chromosome/contig , strand if provided) .TP \fB\-R\fR for \fB\-r\fR option, discard all transcripts that are not fully contained within given range .TP \fB\-U\fR discard single\-exon transcripts .TP \fB\-C\fR discard mRNAs that have no CDS feature .TP \fB\-F\fR keep all attributes from last column of GFF/GTF .TP \fB\-G\fR only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) .TP \fB\-A\fR use the description field from and add it as the value for a 'descr' attribute to the GFF record .TP \fB\-O\fR process non\-transcript GFF records as well (by default non\-transcript records are ignored). .TP \fB\-V\fR discard any mRNAs with CDS having in\-frame stop codons .TP \fB\-H\fR for \fB\-V\fR option, check and adjust the starting CDS phase if the original phase leads to a translation with an in\-frame stop codon .TP \fB\-B\fR for \fB\-V\fR option, single\-exon transcripts are also checked on the opposite strand .TP \fB\-N\fR only show multi\-exon mRNAs if all their introns have the typical splice site consensus ( GT\-AG, GC\-AG or AT\-AC ) .TP \fB\-M\fR discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in\-frame stop codon (only print mRNAs with a fulll, valid CDS) .TP \fB\-E\fR expose (warn about) duplicate transcript IDs and other potential problems with the input GFF/GTF records .TP \fB\-S\fR sort output GFF records by genomic sequence and start coordinate (this option is automatically enabled by \fB\-g\fR option) .TP \fB\-Z\fR merge close exons into a single exon (for intron size<4) .TP \fB\-w\fR write a fasta file with spliced exons for each GFF transcript .TP \fB\-x\fR write a fasta file with spliced CDS for each GFF transcript .TP \fB\-W\fR for \fB\-w\fR and \fB\-x\fR options, also write for each fasta record the exon coordinates projected onto the spliced sequence .TP \fB\-y\fR write a protein fasta file with the translation of CDS for each record .TP \fB\-o\fR the "filtered" GFF records will be written to (use \fB\-o\-\fR for printing to stdout) .TP \fB\-t\fR use in the second column of each GFF output line .HP \fB\-T\fR \fB\-o\fR option will output GTF format instead of GFF3 .PP Invalid argument: \fB\-\-help\fR .PP gffread [\-g | ][\-s ] .IP [\-o ] [\-t ] [\-r [[]:]..] [\-CTVNMAFGRUVBHSZWTOE] [\-w ] [\-x ] [\-y ] [\-i ] Filters and/or converts GFF3/GTF2 records. is a GFF file, use '\-' if the GFF records will be given at stdin .IP Options: .TP \fB\-g\fR full path to a multi\-fasta file with the genomic sequences for all input mappings, OR a directory with single\-fasta files (one per genomic sequence, with file names matching sequence names) .TP \fB\-s\fR is a tab\-delimited file providing this info for each of the mapped sequences: (useful for mRNA/EST/protein mappings with \fB\-A\fR option) .TP \fB\-i\fR discard transcripts having an intron larger than .TP \fB\-r\fR only show transcripts crossing coordinate range .. (on chromosome/contig , strand if provided) .TP \fB\-R\fR for \fB\-r\fR option, discard all transcripts that are not fully contained within given range .TP \fB\-U\fR discard single\-exon transcripts .TP \fB\-C\fR discard mRNAs that have no CDS feature .TP \fB\-F\fR keep all attributes from last column of GFF/GTF .TP \fB\-G\fR only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) .TP \fB\-A\fR use the description field from and add it as the value for a 'descr' attribute to the GFF record .TP \fB\-O\fR process non\-transcript GFF records as well (by default non\-transcript records are ignored). .TP \fB\-V\fR discard any mRNAs with CDS having in\-frame stop codons .TP \fB\-H\fR for \fB\-V\fR option, check and adjust the starting CDS phase if the original phase leads to a translation with an in\-frame stop codon .TP \fB\-B\fR for \fB\-V\fR option, single\-exon transcripts are also checked on the opposite strand .TP \fB\-N\fR only show multi\-exon mRNAs if all their introns have the typical splice site consensus ( GT\-AG, GC\-AG or AT\-AC ) .TP \fB\-M\fR discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in\-frame stop codon (only print mRNAs with a fulll, valid CDS) .TP \fB\-E\fR expose (warn about) duplicate transcript IDs and other potential problems with the input GFF/GTF records .TP \fB\-S\fR sort output GFF records by genomic sequence and start coordinate (this option is automatically enabled by \fB\-g\fR option) .TP \fB\-Z\fR merge close exons into a single exon (for intron size<4) .TP \fB\-w\fR write a fasta file with spliced exons for each GFF transcript .TP \fB\-x\fR write a fasta file with spliced CDS for each GFF transcript .TP \fB\-W\fR for \fB\-w\fR and \fB\-x\fR options, also write for each fasta record the exon coordinates projected onto the spliced sequence .TP \fB\-y\fR write a protein fasta file with the translation of CDS for each record .TP \fB\-o\fR the "filtered" GFF records will be written to (use \fB\-o\-\fR for printing to stdout) .TP \fB\-t\fR use in the second column of each GFF output line .HP \fB\-T\fR \fB\-o\fR option will output GTF format instead of GFF3 .PP debian/gtf_to_sam.10000644000000000000000000000100512231765114011370 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4. .TH GTF_TO_SAM: "1" "May 2011" "gtf_to_sam v1.0.2" "User Commands" .SH NAME gtf_to_sam: \- GTF_TO_SAM .SH SYNOPSIS .B cufflinks [\fIoptions\fR] \fI \fR gtf_to_sam v1.0.2 .SH OPTIONS \fB\-r\fR/\-\-reference\-seq reference fasta file [ default: NULL ] \fB\-F\fR/\-\-raw\-fpkm use FPKM instead of isoform fraction .PP .SH AUTHOR debian/rules0000755000000000000000000000052112231765114010246 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --with autoreconf --parallel override_dh_auto_configure: dh_auto_configure -- LIBS="-lboost_system -lboost_thread" override_dh_auto_clean: dh_auto_clean rm -rf autom4te.cache override_dh_builddeb: dh_builddeb -- -Z xz debian/cufflinks.10000644000000000000000000002005712231765114011242 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4. .TH CUFFLINKS: "1" "May 2011" "cufflinks v1.0.2 '" "User Commands" .SH NAME cufflinks \- Transcript assembly, differential expression, and differential regulation for RNA-Seq .SH DESCRIPTION see online page http://cufflinks.cbcb.umd.edu/manual.html .SH SYNOPSIS .B cufflinks [\fIoptions\fR] \fI\fR .SH OPTIONS .TP \fB\-o\fR/\-\-output\-dir write all output files to this directory [ default: ./ ] .TP \fB\-p\fR/\-\-num\-threads number of threads used during analysis [ default: 1 ] .TP \fB\-G\fR/\-\-GTF quantitate against reference transcript annotations .TP \fB\-g\fR/\-\-GTF\-guide use reference transcript annotation to guide assembly .TP \fB\-M\fR/\-\-mask\-file ignore all alignment within transcripts in this file .TP \fB\-b\fR/\-\-frag\-bias\-correct use bias correction \- reference fasta required [ default: NULL ] .TP \fB\-u\fR/\-\-multi\-read\-correct use 'rescue method' for multi\-reads (more accurate) [ default: FALSE ] .TP \fB\-\-library\-type\fR library prep used for input reads [ default: below ] .SS "Advanced Abundance Estimation Options:" .TP \fB\-m\fR/\-\-frag\-len\-mean average fragment length (unpaired reads only) [ default: 200 ] .TP \fB\-s\fR/\-\-frag\-len\-std\-dev fragment length std deviation (unpaired reads only) [ default: 80 ] .TP \fB\-\-upper\-quartile\-norm\fR use upper\-quartile normalization [ default: FALSE ] .TP \fB\-\-max\-mle\-iterations\fR maximum iterations allowed for MLE calculation [ default: 5000 ] .TP \fB\-\-num\-importance\-samples\fR number of importance samples for MAP restimation [ default: 1000 ] .TP \fB\-\-compatible\-hits\-norm\fR count hits compatible with reference RNAs only [ default: FALSE ] .TP \fB\-\-total\-hits\-norm\fR count all hits for normalization [ default: TRUE ] .SS "Advanced Assembly Options:" .TP \fB\-L\fR/\-\-label assembled transcripts have this ID prefix [ default: CUFF ] .TP \fB\-F\fR/\-\-min\-isoform\-fraction suppress transcripts below this abundance level [ default: 0.10 ] .TP \fB\-j\fR/\-\-pre\-mrna\-fraction suppress intra\-intronic transcripts below this level [ default: 0.15 ] .TP \fB\-I\fR/\-\-max\-intron\-length ignore alignments with gaps longer than this [ default: 300000 ] .TP \fB\-a\fR/\-\-junc\-alpha alpha for junction binomial test filter [ default: 0.001 ] .TP \fB\-A\fR/\-\-small\-anchor\-fraction percent read overhang taken as 'suspiciously small' [ default: 0.09 ] .TP \fB\-\-min\-frags\-per\-transfrag\fR minimum number of fragments needed for new transfrags [ default: 10 ] .TP \fB\-\-overhang\-tolerance\fR number of terminal exon bp to tolerate in introns [ default: 8 ] .TP \fB\-\-max\-bundle\-length\fR maximum genomic length allowed for a given bundle [ default:3500000 ] .TP \fB\-\-min\-intron\-length\fR minimum intron size allowed in genome [ default: 50 ] .TP \fB\-\-trim\-3\-avgcov\-thresh\fR minimum avg coverage required to attempt 3' trimming [ default: 10 ] .TP \fB\-\-trim\-3\-dropoff\-frac\fR fraction of avg coverage below which to trim 3' end [ default: 0.1 ] .SS "Advanced Reference Annotation Guided Assembly Options:" .TP \fB\-\-no\-faux\-reads\fR disable tiling by faux reads [ default: FALSE ] .TP \fB\-\-3\-overhang\-tolerance\fR overhang allowed on 3' end when merging with reference[ default: 600 ] .TP \fB\-\-intron\-overhang\-tolerance\fR overhang allowed inside reference intron when merging [ default: 30 ] .SS "Advanced Program Behavior Options:" .TP \fB\-v\fR/\-\-verbose log\-friendly verbose processing (no progress bar) [ default: FALSE ] .TP \fB\-q\fR/\-\-quiet log\-friendly quiet processing (no progress bar) [ default: FALSE ] .TP \fB\-\-no\-update\-check\fR do not contact server to check for update availability[ default: FALSE ] .SS "Supported library types:" .IP ff\-firststrand ff\-secondstrand ff\-unstranded fr\-firststrand fr\-secondstrand fr\-unstranded (default) transfrags .PP cufflinks v1.0.2 linked against Boost version 104601 \fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR Usage: cufflinks [options] General Options: .TP \fB\-o\fR/\-\-output\-dir write all output files to this directory [ default: ./ ] .TP \fB\-p\fR/\-\-num\-threads number of threads used during analysis [ default: 1 ] .TP \fB\-G\fR/\-\-GTF quantitate against reference transcript annotations .TP \fB\-g\fR/\-\-GTF\-guide use reference transcript annotation to guide assembly .TP \fB\-M\fR/\-\-mask\-file ignore all alignment within transcripts in this file .TP \fB\-b\fR/\-\-frag\-bias\-correct use bias correction \- reference fasta required [ default: NULL ] .TP \fB\-u\fR/\-\-multi\-read\-correct use 'rescue method' for multi\-reads (more accurate) [ default: FALSE ] .TP \fB\-\-library\-type\fR library prep used for input reads [ default: below ] .SS "Advanced Abundance Estimation Options:" .TP \fB\-m\fR/\-\-frag\-len\-mean average fragment length (unpaired reads only) [ default: 200 ] .TP \fB\-s\fR/\-\-frag\-len\-std\-dev fragment length std deviation (unpaired reads only) [ default: 80 ] .TP \fB\-\-upper\-quartile\-norm\fR use upper\-quartile normalization [ default: FALSE ] .TP \fB\-\-max\-mle\-iterations\fR maximum iterations allowed for MLE calculation [ default: 5000 ] .TP \fB\-\-num\-importance\-samples\fR number of importance samples for MAP restimation [ default: 1000 ] .TP \fB\-\-compatible\-hits\-norm\fR count hits compatible with reference RNAs only [ default: FALSE ] .TP \fB\-\-total\-hits\-norm\fR count all hits for normalization [ default: TRUE ] .SS "Advanced Assembly Options:" .TP \fB\-L\fR/\-\-label assembled transcripts have this ID prefix [ default: CUFF ] .TP \fB\-F\fR/\-\-min\-isoform\-fraction suppress transcripts below this abundance level [ default: 0.10 ] .TP \fB\-j\fR/\-\-pre\-mrna\-fraction suppress intra\-intronic transcripts below this level [ default: 0.15 ] .TP \fB\-I\fR/\-\-max\-intron\-length ignore alignments with gaps longer than this [ default: 300000 ] .TP \fB\-a\fR/\-\-junc\-alpha alpha for junction binomial test filter [ default: 0.001 ] .TP \fB\-A\fR/\-\-small\-anchor\-fraction percent read overhang taken as 'suspiciously small' [ default: 0.09 ] .TP \fB\-\-min\-frags\-per\-transfrag\fR minimum number of fragments needed for new transfrags [ default: 10 ] .TP \fB\-\-overhang\-tolerance\fR number of terminal exon bp to tolerate in introns [ default: 8 ] .TP \fB\-\-max\-bundle\-length\fR maximum genomic length allowed for a given bundle [ default:3500000 ] .TP \fB\-\-min\-intron\-length\fR minimum intron size allowed in genome [ default: 50 ] .TP \fB\-\-trim\-3\-avgcov\-thresh\fR minimum avg coverage required to attempt 3' trimming [ default: 10 ] .TP \fB\-\-trim\-3\-dropoff\-frac\fR fraction of avg coverage below which to trim 3' end [ default: 0.1 ] .SS "Advanced Reference Annotation Guided Assembly Options:" .TP \fB\-\-no\-faux\-reads\fR disable tiling by faux reads [ default: FALSE ] .TP \fB\-\-3\-overhang\-tolerance\fR overhang allowed on 3' end when merging with reference[ default: 600 ] .TP \fB\-\-intron\-overhang\-tolerance\fR overhang allowed inside reference intron when merging [ default: 30 ] .SS "Advanced Program Behavior Options:" .TP \fB\-v\fR/\-\-verbose log\-friendly verbose processing (no progress bar) [ default: FALSE ] .TP \fB\-q\fR/\-\-quiet log\-friendly quiet processing (no progress bar) [ default: FALSE ] .TP \fB\-\-no\-update\-check\fR do not contact server to check for update availability[ default: FALSE ] .SS "Supported library types:" .IP ff\-firststrand ff\-secondstrand ff\-unstranded fr\-firststrand fr\-secondstrand fr\-unstranded (default) transfrags debian/watch0000644000000000000000000000012012231765114010212 0ustar version=3 http://cufflinks.cbcb.umd.edu/downloads/cufflinks-([\d\.]*)\.tar\.gz debian/cuffmerge.10000644000000000000000000000216012231765114011214 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4. .TH CUFFMERGE "1" "May 2011" "merge_cuff_asms v1.0.0" "User Commands" .SH NAME cuffmerge \- Merging assemblies .SH DESCRIPTION cuffmerge takes two or more Cufflinks GTF files and merges them into a single unified transcript catalog. Optionally, you can provide the script with a reference GTF, and the script will use it to attach gene names and other metadata to the merged catalog. .SH SYNOPSIS cuffmerge [Options] .SH OPTIONS .TP \fB\-h\fR/\-\-help Prints the help message and exits .TP \fB\-o\fR Directory where merged assembly will be written [ default: ./merged_asm ] .TP \fB\-g\fR/\-\-ref\-gtf An optional "reference" annotation GTF. .TP \fB\-s\fR/\-\-ref\-sequence / Genomic DNA sequences for the reference. .TP \fB\-\-min\-isoform\-fraction\fR <0\-1.0> Discard isoforms with abundance below this [ default: 0.5 ] .TP \fB\-p\fR/\-\-num\-threads Use this many threads to merge assemblies. [ default: 1 ] .TP \fB\-\-keep\-tmp\fR Keep all intermediate files during merge debian/cuffdiff.10000644000000000000000000000577212231765114011041 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4. .TH CUFFDIFF: "1" "May 2011" "cuffdiff" "User Commands" .SH NAME cuffdiff \- find significant changes in transcript expression, splicing, and promoter use .SH SYNOPSIS .B cuffdiff [\fIoptions\fR] \fI \fR[... \fIsampleN_hits.sam\fR] Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam .SH DESCRIPTION see online page http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff .SH OPTIONS .TP \fB\-o\fR/\-\-output\-dir write all output files to this directory [ default: ./ ] .TP \fB\-T\fR/\-\-time\-series treat samples as a time\-series [ default: FALSE ] .TP \fB\-c\fR/\-\-min\-alignment\-count minimum number of alignments in a locus for testing [ default: 10 ] .TP \fB\-\-FDR\fR False discovery rate used in testing [ default: 0.05 ] .TP \fB\-M\fR/\-\-mask\-file ignore all alignment within transcripts in this file [ default: NULL ] .TP \fB\-b\fR/\-\-frag\-bias\-correct use bias correction \- reference fasta required [ default: NULL ] .TP \fB\-u\fR/\-\-multi\-read\-correct use 'rescue method' for multi\-reads (more accurate) [ default: FALSE ] .TP \fB\-N\fR/\-\-upper\-quartile\-norm use upper\-quartile normalization [ default: FALSE ] .TP \fB\-L\fR/\-\-labels comma\-separated list of condition labels .TP \fB\-p\fR/\-\-num\-threads number of threads used during quantification [ default: 1 ] .SS "Advanced Options:" .TP \fB\-\-library\-type\fR Library prep used for input reads [ default: below ] .TP \fB\-m\fR/\-\-frag\-len\-mean average fragment length (unpaired reads only) [ default: 200 ] .TP \fB\-s\fR/\-\-frag\-len\-std\-dev fragment length std deviation (unpaired reads only) [ default: 80 ] .TP \fB\-\-num\-importance\-samples\fR number of importance samples for MAP restimation [ default: 1000 ] .TP \fB\-\-max\-mle\-iterations\fR maximum iterations allowed for MLE calculation [ default: 5000 ] .TP \fB\-\-compatible\-hits\-norm\fR count hits compatible with reference RNAs only [ default: TRUE ] .TP \fB\-\-total\-hits\-norm\fR count all hits for normalization [ default: FALSE ] .TP \fB\-\-poisson\-dispersion\fR Don't fit fragment counts for overdispersion [ default: FALSE ] .TP \fB\-v\fR/\-\-verbose log\-friendly verbose processing (no progress bar) [ default: FALSE ] .TP \fB\-q\fR/\-\-quiet log\-friendly quiet processing (no progress bar) [ default: FALSE ] .TP \fB\-\-no\-update\-check\fR do not contact server to check for update availability[ default: FALSE ] .TP \fB\-\-emit\-count\-tables\fR print count tables used to fit overdispersion [ default: FALSE ] .SS "Supported library types:" .IP ff\-firststrand ff\-secondstrand ff\-unstranded fr\-firststrand fr\-secondstrand fr\-unstranded (default) transfrags .PP debian/patches/0000755000000000000000000000000012231765141010617 5ustar debian/patches/0004-fix-m64-usage-and-lfs.patch0000644000000000000000000000144712231765114016045 0ustar Author: Ben Collins Description: Update configure.ac to not force -m64. Just because the compiler supports it, doesn't mean it can compile natively to it (e.g. on powerpc, you can compile -m64, but there are no headers for it plus it cannot run on 32-bit systems). --- a/configure.ac +++ b/configure.ac @@ -69,11 +69,6 @@ case "${host_cpu}-${host_os}" in i*86-darwin*) CFLAGS="-m64" AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);; - *) - AC_MSG_CHECKING([if gcc accepts -m64]) - CFLAGS="-m64" - AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])], - [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);; esac AC_ARG_ENABLE(vectorize, [ --enable-vectorize Enable GCC auto-vectorization], debian/patches/format-security.patch0000644000000000000000000000115212231765114014774 0ustar Author: Andreas Tille Date: Wed, 22 May 2013 13:27:40 +0200 Description: When building with --format-security (Debhelper 9 hardening) this patch is needed to build successfully --- a/src/locfit/makecmd.c +++ b/src/locfit/makecmd.c @@ -200,7 +200,7 @@ char *cmdline; /* vs is used to store the command line string. */ sprintf(vn,"=clstr%d",clcount); vs = createvar(vn,STSYSTEM,1+strlen(cmdline),VCHAR); - sprintf((char *)vdptr(vs),cmdline); + sprintf((char *)vdptr(vs),"%s",cmdline); /* va is used to store pointers to the command line fields. */ sprintf(vn,"=cline%d",clcount); debian/patches/0003-fix_includes_path.patch0000644000000000000000000000354712231765114015721 0ustar From: Debian Med Packaging Team Date: Fri, 2 Dec 2011 21:21:17 +0000 Subject: fix_includes_path.patch --- src/hits.h | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) --- a/src/hits.h +++ b/src/hits.h @@ -16,7 +16,7 @@ #include -#include +#include #include "common.h" #include "multireads.h" --- a/ax_check_eigen.m4 +++ b/ax_check_eigen.m4 @@ -66,7 +66,7 @@ export EIGEN_CPPFLAGS AC_LANG_PUSH(C++) AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ -@%:@include +@%:@include ]], [[ ]])],[ AC_MSG_RESULT(yes) --- a/configure +++ b/configure @@ -6279,7 +6279,7 @@ cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ -#include +#include int main () --- a/src/abundances.cpp +++ b/src/abundances.cpp @@ -49,7 +49,7 @@ #include "negative_binomial_distribution.h" -#include +#include //using Eigen::MatrixXd; //#ifdef __USE_ISOC99 --- a/src/abundances.h +++ b/src/abundances.h @@ -18,7 +18,7 @@ #include #include -#include +#include #include "hits.h" #include "scaffolds.h" --- a/src/jensen_shannon.h +++ b/src/jensen_shannon.h @@ -14,7 +14,7 @@ #include #include -#include +#include namespace ublas = boost::numeric::ublas; --- a/src/sampling.h +++ b/src/sampling.h @@ -35,7 +35,7 @@ #include #include -#include +#include // Boost Cholesky factorizations in the spirit of lu.hpp // Written by Robbie Vogt, found at: debian/patches/0001-fix_spelling.patch0000644000000000000000000000223112231765114014677 0ustar From: Debian Med Packaging Team Date: 2012-01-05 Subject: fix_spelling --- src/locfit/arith.c | 2 +- src/locfit/lfd.c | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) --- a/src/locfit/arith.c +++ b/src/locfit/arith.c @@ -410,7 +410,7 @@ double (*f)(); INT i; if (l==NULL) { - ERROR(("vvec1 recieved NULL variable\n")); + ERROR(("vvec1 received NULL variable\n")); return NULL; } v = createvar("_vvec1",STHIDDEN,l->n,VDOUBLE); --- a/src/locfit/lfd.c +++ b/src/locfit/lfd.c @@ -78,7 +78,7 @@ INT fp; } } if (access("LFData",W_OK)==-1) - { ERROR(("LFData directory not writeable")); + { ERROR(("LFData directory not writable")); return(0); } } --- a/src/abundances.cpp +++ b/src/abundances.cpp @@ -2901,7 +2901,7 @@ bool AbundanceGroup::calculate_gammas(co vector gammas; - verbose_msg( "Calculating intial MLE\n"); + verbose_msg( "Calculating initial MLE\n"); AbundanceStatus mle_success = gamma_mle(mapped_transcripts, nr_alignments, debian/patches/series0000644000000000000000000000020412231765114012030 0ustar 0004-fix-m64-usage-and-lfs.patch 0001-fix_spelling.patch 0002-bam2samtools.patch 0003-fix_includes_path.patch format-security.patch debian/patches/0002-bam2samtools.patch0000644000000000000000000000073112231765114014623 0ustar From: Debian Med Packaging Team Date: Fri, 2 Dec 2011 21:21:17 +0000 Subject: bam2samtools --- ax_bam.m4 | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) --- a/ax_bam.m4 +++ b/ax_bam.m4 @@ -102,7 +102,7 @@ if test "x$want_bam" = "xyes"; then AC_LANG_PUSH(C++) AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ - @%:@include + @%:@include ]], [[ ]])],[ AC_MSG_RESULT(yes) debian/docs0000644000000000000000000000001712231765114010041 0ustar README AUTHORS debian/compat0000644000000000000000000000000212231765114010366 0ustar 9 debian/compress_gtf.10000644000000000000000000000133712231765114011751 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.39.4. .TH COMPRESS_GTF: "1" "May 2011" "compress_gtf" "User Commands" .SH NAME compress_gtf: \- compress_gtf .SH SYNOPSIS .B compress_gtf [\fIoptions\fR] \fI \fR .SH OPTIONS \fB\-r\fR/\-\-reference\-seq reference fasta file [ default: NULL ] \fB\-F\fR/\-\-raw\-fpkm use FPKM instead of isoform fraction \fB\-U\fR/\-\-union report projective union [ default: OFF ] \fB\-I\fR/\-\-intersection report projective intersection [ default: ON ] .PP .SH SEE ALSO http://cufflinks.cbcb.umd.edu/manual.html