debian/0000755000000000000000000000000011750167550007175 5ustar debian/upstream0000644000000000000000000000063111750044524010753 0ustar Reference: Author: J. F. Abril and R. Guigó and T. Wiehe Title: "gff2aplot: Plotting sequence comparisons" Journal: Bioinformatics Year: 2003 Volume: 19 Number: 18 Pages: 2477-2479 DOI: 10.1093/bioinformatics/btg334 PMID: 4668236 URL: http://bioinformatics.oxfordjournals.org/content/19/18/2477.abstract eprint: http://bioinformatics.oxfordjournals.org/content/19/18/2477.full.pdf+html debian/gff2aplot.10000644000000000000000000001652011110210555011127 0ustar .TH GFF2APLOT 1 "Mon, 21 Mar 2005 21:44:15 -0300" .SH NAME gff2aplot \- Converting GFF files for pairwise alignments to PostScript. .SH SYNOPSIS .B gff2aplot .RI "[options] " .br .SH DESCRIPTION This manual page documents briefly the .B gff2aplot command. .PP \fBgff2aplot\fP is a program that draws color-filled alignment plots from GFF files for that alignment and two sequences annotations. .SH OPTIONS A double dash on itself "--" signals end of the options and start of file names (if present). You can use a single dash "-" as STDIN placeholder. Available options and a short description are listed here: .TP .B \-h, \-\-help Show summary of options. .TP .B \-\-version Shows current version and exits. .TP .B \-v, \-\-verbose Verbose mode, a full report is sent to standard error (default is set to showing only WARNINGS). .TP .B \-V, \-\-logs-filename Report is written to a log file. .TP .B \-q, \-\-quiet Quiet mode, do not show any message/warning to standard error (reporting only ERRORS). .TP .B \-p, \-\-page-size Setting a page size among pre-defined ones see below for a list of available page formats). .TP .B \-\-margin-left .TP .B \-\-margin-right .TP .B \-\-margin-top .TP .B \-\-margin-bottom Setting each page margin to . If no units are provided, points are assumed, you can use points, milimeters, centimeters or inches (pt, mm, cm or in, respectively). .TP .B \-B, \-\-background-color Background color. .TP .B \-F, \-\-foreground-color Foreground color. .TP .B \-T, \-\-title Definning plot title. .TP .B \-t, \-\-subtitle Definning plot subtitle. .TP .B \-X, \-\-x-label Defining X-axis label. .TP .B \-Y, \-\-y-label Defining Y-axis label. .TP .B \-L, \-\-percent-box-label Defining percent-box label. .TP .B \-l, \-\-extra-box-label Definning Extra-Box Label. .TP .B \-x, \-\-x-sequence-coords .TP .B \-S, \-\-start-x-sequence Sets X-sequence first nucleotide. .TP .B \-E, \-\-end-x-sequence Sets X-sequence last nucleotide. .TP .B \-y, \-\--y-sequence-coords .TP .B \-s, \-\-start-y-sequence Sets Y-sequence first nucleotide. .TP .B \-e, \-\-end-y-sequence Sets Y-sequence last nucleotide. .TP .B \-\-x-sequence-zoom .TP .B \-\-y-sequence-zoom .TP .B \-Z, \-\-zoom [ [-S ] [-E ] [-s ] [-e ] ] This option zooms an area you have selected with -S,-E,-s,-e (all 4 are optional). .TP .B \-z, \-\-zoom-area [ [-S ] [-E ] [-s ] [-e ] ] This option marks a zoom area on your plot, but does not make a zoom. .TP .B \-A, \-\-alignment-name Defining which alignment is going to be plotted if you have more than one alignment in your gff input. .TP .B \-N, \-\-x-sequence-name Defining which sequence is going to be plotted at X-axis. .TP .B \-n, \-\-y-sequence-name Defining which sequence is going to be plotted at Y-axis. .TP .B \-r, \-\-aplot-xy-noteq By default X and Y axes have same length, this option disables such behaviour, so X and Y sequence will have axes-lengths proportional to their nucleotide lengths. .TP .B \-R, \-\-xy-axes-scale This option allows to set a different scale between X and Y axes lengths (by default is '1'). Below 1 values make Y larger than X, and larger than 1 result in getting X larger than Y. # Must be explained better. .TP .B \-W, \-\-aln-scale-width Scaling score on width for Aplot lines. .TP .B \-w, \-\-aln-scale-color Scaling score on color for Aplot lines. .TP .B \-K, \-\-show-ribbons Force Ribbons for all features on axes to be: (N)one, (L)ines, (R)ibbons, (B)oth. .TP .B \-G, \-\-show-grid Switches 'on' grid (default is 'off'). .TP .B \-g, \-\-hide-grid Switches 'off' grid (if switched on from customization files). .TP .B \-I, \-\-show-percent-box Switches 'on' Percent box (default is 'off'). .TP .B \-i, \-\-hide-percent-box Switches 'off' Percent box (if set to 'on' on custom files). .TP .B \-O, \-\-show-extra-box Switches 'on' Extra box (default is 'off'). .TP .B \-o, \-\-hide-extra-box Switches 'off' Extra box (if set to 'on' on custom files). .TP .B \-D, \-\-aplot-box-color Aplot main box background color. .TP .B \-d, \-\-percent-box-color Percent box background color. .TP .B \-b, \-\-extra-box-color Extra box background color. .TP .B \-\-nopswarnings Switch off warnings that may appear on the final PostScript figure when X sequence, Y sequence and/or alignment input data is missing. .TP .B \-a, \-\-hide-credits Switch off gff2aplot credits line on plot. .TP .B \-\-debug Reporting variable contents when testing the program. Requires that log report file option was also activated. .TP .B \-\-layout-var '' .TP .B \-\-sequence-var '' .TP .B \-\-source-var '' .TP .B \-\-strand-var '' .TP .B \-\-group-var '' .TP .B \-\-feature-var '' Loading a feature/group/strand/source/sequence/layout customization variable from command-line. You can set several variables by repeating any of these options, i.e.: ... --feature-var 'cds::feature_shape=box' --feature-var 'cds::feature_color=blue' ... .TP .B \-C, \-\-custom-filename Loading customization parameters from a given file (if default ".gff2aplotrc" exists is loaded before it). .TP Those are the colors defined in gff2aplot: + Default Colors: black white. + Color Palette: grey pink magenta violet blue skyblue cyan seagreen green limegreen yellow orange red brown You can get up to nine color shades from Variable Colors with "verydeep", "deep", "verydark", "dark", "light", "verylight", "pale" and "verypale" prefixes, as example: verydeepblue, deepblue, verydarkblue, darkblue, blue, lightblue, verylightblue, paleblue and verypaleblue. + Dynamic colors: gradient rainbow. The following page sizes are available: from A0 to A10, from B0 to B10, 10x14, executive, folio, ledger, legal, letter, quarto, statement and tabloid. .SH ENVIRONMENT VARIABLES There are two environmental variables that can be set by users to their preferences: + You can specify the path where gff2aplot can find the default files with the shell variable "GFF2APLOT_CUSTOMPATH". Default value is the path where you are running gff2aplot. + You can also define the default custom filename you will like with the variable "GFF2APLOT_CUSTOMFILE", program default filename for custom file is ".gff2aplotrc". + Now gff2aplot does not need to write any temporary file, so that previous versions default temporary directory path variable ("GFF2APLOT_TMP") is no longer used. + Setting those vars in Bourne-shell and C-shell: o Using a Bourne-Shell (e.g. bash): export GFF2APLOT_CUSTOMPATH="path" export GFF2APLOT_CUSTOMFILE="file_name" o Using a C-Shell: setenv GFF2APLOT_CUSTOMPATH "path" setenv GFF2APLOT_CUSTOMFILE "file_name" .SH SEE ALSO .BR ali2gff (1), .BR blat2gff (1), .BR parseblast (1), .BR sim2gff (1). .br .SH AUTHOR gff2aplot was written by Josep Francesc ABRIL FERRANDO , Thomas WIEHE and Roderic GUIGO SERRA . .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/examples0000644000000000000000000000001311517543703010727 0ustar examples/* debian/sim2gff.10000644000000000000000000000226111110210555010575 0ustar .TH SIM2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300" .SH NAME sim2gff \- Converts SIM file into GFF formatted records .SH SYNOPSIS .B sim2gff .RI "[-frxyHh] sim_file > gff_file" .br .SH DESCRIPTION This manual page documents briefly the .B sim2gff command. .PP \fBsim2gff\fP is a program written in Perl that converts SIM file into GFF formatted records (for use with gff2aplot and gff2javaplot). .SH OPTIONS .TP .B \-h, \-\-help Show summary of options. .TP .B \-f Output is written to a file named .gff. .TP .B \-r Interchange the order of sequences (Seq1 on y-axis, Seq2 on x-axis). .TP .B \-x Specify the species name for species1 (default: "Seq1"). .TP .B \-y Specify the species name for species2 (default: "Seq2"). .TP .B \-H Use the fasta file headers for species labels. .SH EXIT STATUS The following perl-like exit status are returned: .PP .B 0 Error .PP .B 1 Successful completion .SH SEE ALSO .BR ali2gff (1), .BR blat2gff (1), .BR gff2aplot (1), .BR parseblast (1). .br .SH AUTHOR sim2gff was written by Thomas Wiehe . .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/source/0000755000000000000000000000000011353060303010460 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000004211110210555010024 0ustar README doc/GFF2APLOT_MANUAL.ps.gz debian/ali2gff.10000644000000000000000000000167611110210555010563 0ustar .TH ALI2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300" .SH NAME ali2gff \- Module to translate a MUMmer output files into gff formatted output. .SH SYNOPSIS .B ali2gff .RI "[-r] [-t <.|0|1|2>] [-x ] [-y ] [-H] [-f] [-h] " .br .SH OPTIONS .TP .B \-h, \-\-help Show summary of options. .TP .B \-r Interchange the order of sequences (sequence 1 on y-axis, sequence 2 on x-axis). .TP .B \-t <.|0|1|2> Put label 'frame' in gff output. .TP .B \-x Specify the species name for species1 (default: "Seq1"). .TP .B \-y Specify the species name for species2 (default: "Seq2"). .TP .B \-i Ignore full sequence identities. .TP .B \-f Write output to file. .SH SEE ALSO .BR blat2gff (1), .BR gff2aplot (1), .BR parseblast (1), .BR sim2gff (1). .br .SH AUTHOR ali2gff was written by Steffi Gebauer-Jung. .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/copyright0000644000000000000000000000261611750165447011140 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: GFF2APLOT Upstream-Contact: Josep Francesc ABRIL FERRANDO Source: http://genome.imim.es/software/gfftools/GFF2APLOT.html Files: * Copyright: 1999-2003 Josep Francesc ABRIL FERRANDO Thomas WIEHE Roderic GUIGO SERRA License: GPL-2+ Files: debian/* Copyright: 2005-2008 Nelson A. de Oliveira 2011-2012 Andreas Tille License: GPL-2+ 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. debian/compat0000644000000000000000000000000211750166003010363 0ustar 9 debian/install0000644000000000000000000000001611517544422010561 0ustar bin/* usr/bin debian/control0000644000000000000000000000604711750166014010601 0ustar Source: gff2aplot Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Nelson A. de Oliveira , Andreas Tille Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gff2aplot/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gff2aplot/trunk/ Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html Package: gff2aplot Architecture: any Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends} Suggests: postscript-viewer, gff2ps Description: pair-wise alignment-plots for genomic sequences in PostScript A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot: * Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets. * All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file. * Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement. * All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients. * Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes. * The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error. * gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape. * You can draw different alignments on same alignment plot and distinguish them by using different colors for each. * Shape dictionary has been expanded, so that further feature shapes are now available (see manual). * Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows to show color pseudo-blending when horizontal and vertical ribbons overlap. debian/parseblast.10000644000000000000000000001410011110210555011373 0ustar .TH PARSEBLAST 1 "Mon, 21 Mar 2005 21:44:15 -0300" .SH NAME parseblast \- Filtering High-scoring Segment Pairs (HSPs) from WU/NCBI BLAST. .SH SYNOPSIS .B parseblast .RI "[options] " .br .SH DESCRIPTION This manual page documents briefly the .B parseblast command. .PP Different output options are available, the most important here are those allowing to write HSPs in GFF format (GFFv1, GFFv2 or APLOT). Sequences can be included in the GFF records as a comment field. Furthermore, this script can output also the alignments for each HSP in ALN, MSF or tabular formats. \fBNOTE\fP - If first line from blast program output (the one containing which flavour has been run, say here BLASTN, BLASTP, BLASTX, TBLASTN or TBLASTX), is missing, the program assumes that it contains BLASTN HSP records. So that, ensure that you feed the parseblast script with a well formatted BLAST file. Sometimes there are no spaces between the HSP coords and its sequence, as it sometimes happens in Web-Blast or Paracel-Blast outputs. Now those records are processed ok and that HSP is retrieved as well as "standard" ones. \fBWARNING\fP - Frame fields from GFF records generated with parseblast contain BLAST frame (".","1","2","3") instead of the GFF standard values (".","0","1","2"). As the frame for reverse strand must be recalculated from the original sequence length, we suggest users to post-process the GFF output from this script with a suitable filter that fix the frames (in case that the program that is going to use the GFF records will not work with the original BLAST frames). We provide the command-line option "--no-frame" to set frames to "." (meaning that there is no frame). .SH OPTIONS parseblast prints output in "HSP" format by default (see below). It takes input from or single/multiple files, and writes its output to , so user can redirect to a file but he also could use the program as a filter within a pipe. "-N", "-M", "-P", "-G", "-F", "-A" and "-X" options (also the long name versions for each one) are mutually exclusive, and their precedence order is shown above. .TP .B GFF OPTIONS: .TP .B \-G, \-\-gff Prints output in GFFv1 format. .TP .B \-F, \-\-fullgff Prints output in GFFv2 "alignment" format ("target"). .TP .B \-A, \-\-aplot Prints output in pseudo-GFF APLOT "alignment" format. .TP .B \-S, \-\-subject Projecting GFF output by SUBJECT (default by QUERY). .TP .B \-Q, \-\-sequence Append query and subject sequences to GFF record. .TP .B \-b, \-\-bit-score Set field to Bits (default Alignment Score). .TP .B \-i, \-\-identity-score Set field to Identities (default Alignment). .TP .B \-s, \-\-full-scores Include all scores for each HSP in each GFF record. .TP .B \-u, \-\-no-frame Set all frames to "." (GFF for not available frames). .TP .B \-t, \-\-compact-tags Target coords+strand+frame in short form (NO GFFv2!). .TP .B ALIGNMENT OPTIONS: .TP .B \-P, \-\-pairwise Prints pairwise alignment for each HSP in TBL format. .TP .B \-M, \-\-msf Prints pairwise alignment for each HSP in MSF format. .TP .B \-N, \-\-aln Prints pairwise alignment for each HSP in ALN format. .TP .B \-W, \-\-show-coords Adds start/end positions to alignment output. .TP .B GENERAL OPTIONS: .TP .B \-X, \-\-expanded Expanded output (producing multiline output records). .TP .B \-c, \-\-comments Include parameters from blast program as comments. .TP .B \-n, \-\-no-comments Do not print "#" lines (raw output without comments). .TP .B \-v, \-\-verbose Warnings sent to . .TP .B \-\-version Prints program version and exits. .TP .B \-h, \-\-help Shows this help and exits. .SH OUTPUT FORMATS: "S_" stands for "Subject_Sequence" and "Q_" for "Query_Sequence". name is taken from input blast file. are calculated from and positions on original blast file. is obtained from the blast file if is present else is set to ".". is set to Alignment Score by default, you can change it with "-b" and "-i". If "-S" or "--subject" options are given, then QUERY fields are referred to SUBJECT and SUBJECT fields are relative to QUERY (this only available for GFF output records). Dots ("...") mean that record description continues in the following line, but such record is printed as a single line record by parseblast. .PP .B [HSP] <- (This is the DEFAULT OUTPUT FORMAT) : ... ... ... ... : ... ... : ... ... : .PP .B [GFF] hsp .PP .B [FULL GFF] <- (GFF showing alignment data) hsp ... ... Target "" ... ... E_value Strand Frame .PP .B [APLOT] <- (GFF format enhanced for APLOT program) : hsp : : ... ... : : : ... ... # E_value .PP .B [EXPANDED] MATCH(): x SCORE(): BITSC(): EXPEC(): Psum() IDENT(): / : % T_GAP(): FRAME(): / STRND(): / MXLEN(): QUERY(): length : gaps : ... ... : : : SBJCT(): length : gaps : ... ... : : : .SH SEE ALSO .BR ali2gff (1), .BR blat2gff (1), .BR gff2aplot (1), .BR sim2gff (1). .br .SH AUTHOR parseblast was written by Josep F. Abril . .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/patches/0000755000000000000000000000000011750167112010616 5ustar debian/patches/series0000644000000000000000000000007611750166574012051 0ustar 02-blat2gff.diff 03-parseblast.diff use-dpkg-buildflags.patch debian/patches/03-parseblast.diff0000644000000000000000000000135011750166231014030 0ustar Author: Nelson A. de Oliveira Date: 2005-03-22 18:39:54 -0300 --- gff2aplot-2.0.orig/src/parseblast.pl +++ gff2aplot-2.0/src/parseblast.pl @@ -827,7 +827,7 @@ }; }; # $prt # - ( $program, $version ) = split /\s+/og, $str, 2; + ( $program, $version ) = split /\s+/o, $str, 2; # typeQ/typeS: 0 for proteins - 1 for nucleic acids. # Amino Acids vs Amino Acids @@ -863,7 +863,7 @@ $prog_params = "#\n# $program $version\n#"; $query_name = $db_name = ''; }; - ( $seqname, $descr ) = split /\s+/og, $str, 2; + ( $seqname, $descr ) = split /\s+/o, $str, 2; $seqname =~ s/^\s*>//o; $seqname =~ s/\s|:|\|/_/og; $seqname .= "_" . ( $index++ ); debian/patches/use-dpkg-buildflags.patch0000644000000000000000000000071511750167112015473 0ustar Description: Use build flags from environment (dpkg-buildflags). Necessary for hardening flags. Author: Andreas Tille Date: Wed, 02 May 2012 10:20:01 +0200 --- gff2aplot-2.0.orig/src/ali2gff/Makefile +++ gff2aplot-2.0/src/ali2gff/Makefile @@ -22,7 +22,7 @@ all : ali2gff ali2gff : ali2gff.c ali2gff.h Makefile - @$(CC) -o ali2gff ali2gff.c; + @$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o ali2gff ali2gff.c; @chmod 755 ali2gff clean : debian/patches/02-blat2gff.diff0000644000000000000000000000216311750166242013363 0ustar Author: Nelson A. de Oliveira Date: 2005-03-21 22:46:49 -0300 --- gff2aplot-2.0.orig/src/blat2gff.pl +++ gff2aplot-2.0/src/blat2gff.pl @@ -82,7 +82,7 @@ my @f = (); next unless /^\d/o; chomp; - @f = split /\s+/og, $_; + @f = split /\s+/o, $_; do { # ensure that there are 21 fields print STDERR "### NOT enough fields for this record:\n##### @f \n"; next; @@ -111,9 +111,9 @@ $gff{T_FRAME} = &get_frame( $gff{T_STRAND}, $gff{T_LEN}, $gff{T_ORI}, $gff{T_END} ); $gff{B_NUM} = $f[ $blat{B_NUM} ]; - @{ $gff{B_LEN} } = split /,/og, $f[ $blat{B_LEN} ]; - @{ $gff{B_QPOS} } = split /,/og, $f[ $blat{B_QPOS} ]; - @{ $gff{B_TPOS} } = split /,/og, $f[ $blat{B_TPOS} ]; + @{ $gff{B_LEN} } = split /,/o, $f[ $blat{B_LEN} ]; + @{ $gff{B_QPOS} } = split /,/o, $f[ $blat{B_QPOS} ]; + @{ $gff{B_TPOS} } = split /,/o, $f[ $blat{B_TPOS} ]; printf STDOUT "# " . $GFFstring, $gff{Q_NAME}, "BLAT", "$gff{Q_LEN}:$gff{T_LEN}", $gff{Q_ORI}, $gff{Q_END}, 0, $gff{Q_STRAND}, $gff{Q_FRAME}, "$gff{T_NAME}.$gff{GROUP}.$rec_cnt", $gff{T_ORI}, debian/manpages0000644000000000000000000000001311517543665010713 0ustar debian/*.1 debian/watch0000644000000000000000000000013711110210555010207 0ustar version=3 ftp://genome.imim.es/pub/software/gff_tools/gff2aplot/gff2aplot-v(.*)\_(.*)\.tar\.gz debian/dirs0000644000000000000000000000001011110210555010030 0ustar usr/bin debian/changelog0000644000000000000000000000462311750167473011060 0ustar gff2aplot (2.0-7) unstable; urgency=low * debian/upstream: Added citation information * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs-Svn - Removed cdbs+quilt from Build-Depends * debian/copyright: Rewritten to DEP5 * debian/patches/use-dpkg-buildflags.patch: Use build flags from environment to enable hardening * debhelper 9 (control+compat) -- Andreas Tille Tue, 01 May 2012 22:37:01 +0200 gff2aplot (2.0-6) unstable; urgency=low * debian/control - Added myself as Uploader - Standards-Version: 3.9.1 (no changes needed) - debhelper 7 (actually >= 7.1) - Fixed Spelling of Debian Med team - Build-Depends: removed cdbs, added quilt * debian/source/format: 3.0 (quilt) * debian/rules: rewritten to use dh * debian/patches: use quilt * debian/patches/01-makefile.diff: Removed because unneeded with current packaging * debian/{examples,install,manpages}: added -- Andreas Tille Tue, 25 Jan 2011 13:32:41 +0100 gff2aplot (2.0-5) unstable; urgency=low * Updated Standards-Version; * Changed Maintainer to the Debian-Med Packaging Team; * Added new Homepage field; * Added Vcs-* fields. -- Nelson A. de Oliveira Sun, 24 Feb 2008 00:25:43 -0300 gff2aplot (2.0-4) unstable; urgency=low * Updated patches/01-makefile.diff, so ali2gff doesn't get stripped when using DEB_BUILD_OPTIONS=nostrip (Closes: #436975); * Updated maintainer email; * Updated Standards-Version to 3.7.2; * Updated compat version to 5; * Updated watch file. -- Nelson A. de Oliveira Thu, 09 Aug 2007 17:16:13 -0300 gff2aplot (2.0-3) unstable; urgency=low * Not using DEB_AUTO_UPDATE_DEBIAN_CONTROL of CDBS anymore; * Updated Standards-Version to 3.6.1.1 (no modifications needed). -- Nelson A. de Oliveira Thu, 2 Jun 2005 20:26:19 -0300 gff2aplot (2.0-2) unstable; urgency=low * debian/rules: fix DEB_AUTO_UPDATE_DEBIAN_CONTROL position; * debian/control: changed ps-viewer to postscript-viewer on Suggests field; * debian/control: corrected indentation of description; * Included watch file. -- Nelson A. de Oliveira Tue, 12 Apr 2005 14:16:53 -0300 gff2aplot (2.0-1) unstable; urgency=low * Initial Release (Closes: #300828) -- Nelson A. de Oliveira Mon, 21 Mar 2005 20:30:45 -0300 debian/rules0000755000000000000000000000056611750164674010270 0ustar #!/usr/bin/make -f # debian/rules file for gff2aplot using dh # Andreas Tille # GPL %: dh $@ # Upstream is missing to clean some files override_dh_auto_clean: rm -f src/ali2gff/ali2gff bin/ali2gff # We need to rename some *.pl files override_dh_auto_install: for script in `find bin -name "*.pl"` ; do mv $$script bin/`basename $$script .pl` ; done debian/blat2gff.10000644000000000000000000000074411110210555010733 0ustar .TH BLAT2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300" .SH NAME blat2gff \- Converts BLAT output files to GFF formatted files .SH SYNOPSIS .B blat2gff .RI " < inputfile > outputfile" .br .SH SEE ALSO .BR ali2gff (1), .BR gff2aplot (1), .BR parseblast (1), .BR sim2gff (1). .br .SH AUTHOR blat2gff was written by Josep Francesc ABRIL FERRANDO . .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others).