[med-svn] r1164 - in trunk/packages/tacg/trunk: . debian debian/patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Jan 19 03:13:53 UTC 2008
Author: charles-guest
Date: 2008-01-19 03:13:42 +0000 (Sat, 19 Jan 2008)
New Revision: 1164
Added:
trunk/packages/tacg/trunk/debian/
trunk/packages/tacg/trunk/debian/README.Debian
trunk/packages/tacg/trunk/debian/changelog
trunk/packages/tacg/trunk/debian/compat
trunk/packages/tacg/trunk/debian/control
trunk/packages/tacg/trunk/debian/copyright
trunk/packages/tacg/trunk/debian/dirs
trunk/packages/tacg/trunk/debian/docs
trunk/packages/tacg/trunk/debian/examples
trunk/packages/tacg/trunk/debian/install
trunk/packages/tacg/trunk/debian/manpages
trunk/packages/tacg/trunk/debian/patches/
trunk/packages/tacg/trunk/debian/patches/series
trunk/packages/tacg/trunk/debian/patches/to-build-with-gcc4.patch
trunk/packages/tacg/trunk/debian/rules
trunk/packages/tacg/trunk/debian/tacg.doc-base.EX
trunk/packages/tacg/trunk/debian/watch.ex
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/tacg/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/tacg/trunk/debian/README.Debian
===================================================================
--- trunk/packages/tacg/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/tacg/trunk/debian/README.Debian 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,6 @@
+tacg for Debian
+---------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 18 Jan 2008 17:47:56 +0900
Added: trunk/packages/tacg/trunk/debian/changelog
===================================================================
--- trunk/packages/tacg/trunk/debian/changelog (rev 0)
+++ trunk/packages/tacg/trunk/debian/changelog 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,6 @@
+tacg (4.1.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 18 Jan 2008 17:47:56 +0900
+
Added: trunk/packages/tacg/trunk/debian/compat
===================================================================
--- trunk/packages/tacg/trunk/debian/compat (rev 0)
+++ trunk/packages/tacg/trunk/debian/compat 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1 @@
+5
Added: trunk/packages/tacg/trunk/debian/control
===================================================================
--- trunk/packages/tacg/trunk/debian/control (rev 0)
+++ trunk/packages/tacg/trunk/debian/control 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,30 @@
+Source: tacg
+Section: science
+Priority: optional
+Maintainer: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: cdbs, autotools-dev, automake1.10, autoconf
+Standards-Version: 3.7.3
+
+Package: tacg
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Enhances: nedit
+Description: command line program for finding patterns in nucleic acids
+ tacg is a character-based, command line tool for unix-like operating systems
+ for pattern-matching in nucleic acids and performing some of the basic protein
+ manipulations. It was originally designed for restriction enzyme analysis of
+ DNA, but has been extended to other types of matching. It now handles
+ degenerate sequence input in a variety of matching approaches, as well as
+ patterns with errors, regular expressions and TRANSFAC-formatted matrices.
+ .
+ It was designed to be a grep for DNA and like the original grep, its
+ capabilities have grown so that now the author has to keep calling up the help
+ page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
+ application in any sense. However, it's existance as a strictly command-line
+ tool lends itself well to Webification and wrapping by various GUI tools and
+ it is now distributed with a web interface form and a Perl CGI handler.
+ Additionally, it can easily be integrated into editors that support shell
+ commands such as nedit.
+ .
+ The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
+ BMC Bioinformatics. 3:8 http://www.biomedcentral.com/1471-2105/3/8
Added: trunk/packages/tacg/trunk/debian/copyright
===================================================================
--- trunk/packages/tacg/trunk/debian/copyright (rev 0)
+++ trunk/packages/tacg/trunk/debian/copyright 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,135 @@
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Charles Plessy <charles-debian-nospam at plessy.org>
+X-Debianized-Date: Fri, 18 Jan 2008 17:47:56 +0900.
+X-Source-Downloaded-From: http://sourceforge.net/projects/tacg
+X-Upstream-Author: Harry Mangalam, tacg Informatics
+
+Files: debian/*
+Copyright: © 2008, Charles Plessy <charles-debian-nospam at plessy.org>
+License: Same as tacg itself.
+
+File: install-sh
+X-Comment: This comes from X11R5 (mit/util/scripts/install.sh).
+Copyright: © 1991 by the Massachusetts Institute of Technology
+License: MIT
+ Permission to use, copy, modify, distribute, and sell this software and its
+ documentation for any purpose is hereby granted without fee, provided that
+ the above copyright notice appear in all copies and that both that
+ copyright notice and this permission notice appear in supporting
+ documentation, and that the name of M.I.T. not be used in advertising or
+ publicity pertaining to distribution of the software without specific,
+ written prior permission. M.I.T. makes no representations about the
+ suitability of this software for any purpose. It is provided "as is"
+ without express or implied warranty.
+
+Files: getopt*
+Copyright: © 1987,88,89,90,91,92,93,94,95,96,98,99,2000,2001 Free Software Foundation, Inc.
+X-Comment: This file is part of the GNU C Library.
+License: LGPL-2.1+
+ The GNU C Library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ The GNU C Library 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
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+X-Comment: On Debian systems, the complete text of the GNU Lesser General Public License
+can be found in `/usr/share/common-licenses/LGPL-2.1'.
+
+Files: seqio.c
+Copyright: © 1996 James Knight at Univ. of California, Davis
+License:
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation is hereby granted, subject to the following
+ restrictions and understandings:
+ .
+ 1) Any copy of this software or any copy of software derived
+ from it must include this copyright notice in full.
+ .
+ 2) All materials or software developed as a consequence of the
+ use of this software or software derived from it must duly
+ acknowledge such use, in accordance with the usual standards
+ of acknowledging credit in academic research.
+ .
+ 3) The software may be used freely by anyone for any purpose,
+ commercial or non-commercial. That includes, but is not
+ limited to, its incorporation into software sold for a profit
+ or the development of commercial software derived from it.
+ .
+ 4) This software is provided AS IS with no warranties of any
+ kind. The author shall have no liability with respect to the
+ infringement of copyrights, trade secrets or any patents by
+ this software or any part thereof. In no event will the
+ author be liable for any lost revenue or profits or other
+ special, indirect and consequential damages.
+
+File: strsep.c
+Copyright: © 1998 by Gray Watson
+License:
+ Permission to use, copy, modify, and distribute this software for
+ any purpose and without fee is hereby granted, provided that the
+ above copyright notice and this permission notice appear in all
+ copies, and that the name of Gray Watson not be used in advertising
+ or publicity pertaining to distribution of the document or software
+ without specific, written prior permission.
+ .
+ Gray Watson makes no representations about the suitability of the
+ software described herein for any purpose. It is provided "as is"
+ without express or implied warranty.
+ .
+ The author may be contacted at gray.watson at letters.com
+
+Files: *
+Copyright: © 1994-2005 by Harry Mangalam, tacg Informatics
+ Permission to use, copy, modify, and distribute this software and its
+ documentation is hereby granted, subject to the following restrictions
+ and understandings:
+ .
+ 1) Any copy of this software or any copy of software derived
+ from it must include this copyright notice in full.
+ .
+ 2) All materials or software developed as a consequence of the
+ use of this software or software derived from it must duly
+ acknowledge such use, in accordance with the usual standards
+ of acknowledging credit in academic research.
+ .
+ The use of tacg may be cited as:
+ Mangalam, HJ. (2002) tacg, a grep for DNA.
+ BMC Bioinformatics 2002, 3:8.
+ tacg Informatics. hjm at tacgi.com, 949 856 2847
+ .
+ The latest version of the software may be obtained at:
+ http://tacg.sf.net or by writing the author.
+ .
+ 3) The software may be used by anyone for any purpose, subject to the
+ Free Software Foundation's General Public License, a copy of which
+ should have been included with this distribution (see the file
+ COPYING in the source distribution).
+ If it was not included with this distribution, a copy may be obtained
+ from: http://www.gnu.org/copyleft/gpl.html .
+ .
+ Those persons or organizations wanting to use code derived from tacg
+ in proprietary applications so as not to have their code 'infected'
+ by the FSF GPL have the option to license the code directly from from
+ the author under a separate license. This option takes advantage of
+ the so-called Dual Licensing policy, which is approved by the FSF.
+ .
+ 4) This software is not meant to be used as a sole tool to design
+ recombinant molecules for theraputic use. While it is accurate to
+ the best of my knowledge about the results it gives, it has not
+ been validated to this stringency yet. Hence the release of the
+ source code.
+ .
+ 5) This software is provided AS IS with NO WARRANTIES OF ANY KIND. The
+ author shall have no liability with respect to the infringement of
+ copyrights, trade secrets or any patents by this software or any part
+ thereof. In no event will the author be liable for any lost revenue
+ or profits or other special, indirect and consequential damages.
+X-Comment: On Debian systems, the complete text of the GNU General Public License
+ can be found in `/usr/share/common-licenses/GPL'.
Added: trunk/packages/tacg/trunk/debian/dirs
===================================================================
--- trunk/packages/tacg/trunk/debian/dirs (rev 0)
+++ trunk/packages/tacg/trunk/debian/dirs 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,2 @@
+usr/bin
+usr/sbin
Added: trunk/packages/tacg/trunk/debian/docs
===================================================================
--- trunk/packages/tacg/trunk/debian/docs (rev 0)
+++ trunk/packages/tacg/trunk/debian/docs 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,6 @@
+NEWS
+README
+Docs/tacg4.0.main.html
+Docs/tacg4.help.html
+Docs/tacg4.man.html
+Docs/tacg4.xman.html
Added: trunk/packages/tacg/trunk/debian/examples
===================================================================
--- trunk/packages/tacg/trunk/debian/examples (rev 0)
+++ trunk/packages/tacg/trunk/debian/examples 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,25 @@
+Seqs/hlef.seq
+Seqs/hsp.cluster.1000.fasta
+Seqs/humanprlreceptor.gb
+Seqs/humanprlreceptor.gcg
+Seqs/humprlrec.pep.fasta
+Seqs/test.embl
+Seqs/test.fasta
+Seqs/test.fitch
+Seqs/test.gb
+Seqs/test.gcg
+Seqs/test.ig
+Seqs/test.ig-b
+Seqs/test.m-embl
+Seqs/test.m-fasta
+Seqs/test.m-gb
+Seqs/test.m-ig
+Seqs/test.m-ig-b
+Seqs/test.m-msf
+Seqs/test.m-nbrf
+Seqs/test.m-paup
+Seqs/test.m-pir
+Seqs/test.nbrf
+Seqs/test.pir
+Seqs/test.strider
+Docs/nedit.macros
Added: trunk/packages/tacg/trunk/debian/install
===================================================================
--- trunk/packages/tacg/trunk/debian/install (rev 0)
+++ trunk/packages/tacg/trunk/debian/install 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1 @@
+Data/*.data /usr/share/tacg
Added: trunk/packages/tacg/trunk/debian/manpages
===================================================================
--- trunk/packages/tacg/trunk/debian/manpages (rev 0)
+++ trunk/packages/tacg/trunk/debian/manpages 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1 @@
+Docs/tacg.1
Added: trunk/packages/tacg/trunk/debian/patches/series
===================================================================
--- trunk/packages/tacg/trunk/debian/patches/series (rev 0)
+++ trunk/packages/tacg/trunk/debian/patches/series 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,2 @@
+to-build-with-gcc4.patch
+path-to-data.patch
Added: trunk/packages/tacg/trunk/debian/patches/to-build-with-gcc4.patch
===================================================================
--- trunk/packages/tacg/trunk/debian/patches/to-build-with-gcc4.patch (rev 0)
+++ trunk/packages/tacg/trunk/debian/patches/to-build-with-gcc4.patch 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,72 @@
+--- a/tacg.h
++++ b/tacg.h
+@@ -168,23 +168,6 @@
+ #define _XOPEN_SOURCE 500
+
+
+-/* ------------------ Global declarations ------------------------ */
+-
+-extern struct RE_struct *RE;
+-extern struct ORF_struct *ORFs[6];
+-extern struct Digest_Data *DD;
+-extern struct Prox_struct PP[10];
+-extern struct PW_struct *PosWin;
+-extern struct Clone_struct Clone_S[MAX_NUM_CLONE_RANGES];
+-extern struct Rule_struct *Rules;
+-extern struct flag_struct F;
+-extern struct SE_struct *SelEnz[];
+-extern char *sequence;
+-extern long *Degen_Log;
+-extern char *optarg;
+-extern int optind, opterr, optopt;
+-
+-
+ /* --------------------- Struct Declarations -------------------------- */
+
+
+@@ -438,6 +421,23 @@
+ };
+
+
++/* ------------------ Global declarations ------------------------ */
++
++extern struct RE_struct *RE;
++extern struct ORF_struct *ORFs[6];
++extern struct Digest_Data *DD;
++extern struct Prox_struct PP[10];
++extern struct PW_struct *PosWin;
++extern struct Clone_struct Clone_S[MAX_NUM_CLONE_RANGES];
++extern struct Rule_struct *Rules;
++extern struct flag_struct F;
++extern struct SE_struct *SelEnz[];
++extern char *sequence;
++extern long *Degen_Log;
++extern char *optarg;
++extern int optind, opterr, optopt;
++
++
+ /*********************** Function Prototype Declarations ************************/
+
+ /* fill_out_sum duplicates the degeneracy the correct # of times in the array 'sum[]' for submission
+--- a/SeqFuncs.c
++++ b/SeqFuncs.c
+@@ -1153,7 +1153,7 @@
+ should have been functionized long ago */
+
+ void LinearMap(long seq_len, int basesPerLine, int NumREs, char *sequence, int max_okline,
+- char Codons[][][], int codon_Table, int *Protos) {
++ char Codons[8][64][7], int codon_Table, int *Protos) {
+
+ /* Declarations */
+ int i, d, k, mm=0, rc, n_letters=0, Xn=0, okline, HTML, spacer, spacermod, stanzaspace,
+--- a/SetFlags.c
++++ b/SetFlags.c
+@@ -826,7 +826,7 @@
+ "\nThis is free software; see the source for copying conditions. There is NO"
+ "\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n",
+ TACG_VERSION);
+- fprintf (stdout, " Executable built: %s \n on kernel: %s\n GCC version: %s\n", TACG_BUILD_DATE, TACG_BUILD_PLATFORM, TACG_GCC_VER);
++ /*fprintf (stdout, " Executable built: %s \n on kernel: %s\n GCC version: %s\n", TACG_BUILD_DATE, TACG_BUILD_PLATFORM, TACG_GCC_VER);*/
+ exit(1);
+ break;
+
Added: trunk/packages/tacg/trunk/debian/rules
===================================================================
--- trunk/packages/tacg/trunk/debian/rules (rev 0)
+++ trunk/packages/tacg/trunk/debian/rules 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+DEB_AUTO_UPDATE_AUTOMAKE=1.10
+DEB_AUTO_UPDATE_ACLOCAL=1.10
+DEB_AUTO_UPDATE_AUTOCONF=2.61
+
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
Property changes on: trunk/packages/tacg/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/tacg/trunk/debian/tacg.doc-base.EX
===================================================================
--- trunk/packages/tacg/trunk/debian/tacg.doc-base.EX (rev 0)
+++ trunk/packages/tacg/trunk/debian/tacg.doc-base.EX 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,22 @@
+Document: tacg
+Title: Debian tacg Manual
+Author: <insert document author here>
+Abstract: This manual describes what tacg is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/tacg/tacg.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/tacg/tacg.ps.gz
+
+Format: text
+Files: /usr/share/doc/tacg/tacg.text.gz
+
+Format: HTML
+Index: /usr/share/doc/tacg/html/index.html
+Files: /usr/share/doc/tacg/html/*.html
+
+
Added: trunk/packages/tacg/trunk/debian/watch.ex
===================================================================
--- trunk/packages/tacg/trunk/debian/watch.ex (rev 0)
+++ trunk/packages/tacg/trunk/debian/watch.ex 2008-01-19 03:13:42 UTC (rev 1164)
@@ -0,0 +1,22 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php tacg-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/tacg-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/tacg-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for debscripts >= 2.9
+# http://sf.net/tacg/tacg-(.*)\.tar\.gz
+
+
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