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Bug#461504: marked as done (ITP: tacg -- command line program for finding patterns in nucleic acids)

Your message dated Tue, 25 May 2010 23:18:50 +0900
with message-id <20100525141850.GC8722@kunpuu.plessy.org>
and subject line Will not package tacg.
has caused the Debian Bug report #461504,
regarding ITP: tacg -- command line program for finding patterns in nucleic acids
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
461504: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=461504
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>

  Package name    : tacg
  Version         : 4.1.0
  Upstream Author : Harry Mangalam, tacg Informatics
  URL             : http://sourceforge.net/projects/tacg
  License         : GPL and others
  Programming Lang: C (tacg), Perl (CGI)
  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

I had to apply an ugly patch in order to compile it with gcc4. Because I am not
a C programmer, I barely understand what I did, so I would appreciate comments
on the patch:

http://svn.debian.org/wsvn/debian-med/trunk/packages/tacg/trunk/debian/patches/to-build-with-gcc4.patch?op=file&rev=0&sc=0

This is a low-quality patch, but it works. The modificaiton of tacg.h was
made according to what I found on the mailing lists, and seems to make
sense. The modification of SeqFuncs.c is completely heuristic; I used the
same numbers as in tacg.h. The modification of SetFlags.c is a quick
workaround that does not solve the real problem.

Also, you can consult the full copyright file in the same repository:

http://svn.debian.org/wsvn/debian-med/trunk/packages/tacg/trunk/debian/copyright?op=file&rev=0&sc=0

I use tacg to search for oligonucleotides in sequence reads: I need to allow
mismatches, and want to detect if I (unfortunatley) cloned concatemer
artefacts. If you know a better tool, let me know !

Have a nice day,

-- 
Charles Plessy
Debian-Med packaging team
Wakō, Saitama, Japan

--- End Message ---
--- Begin Message --- 
Since nobody reacted to the patch that I posted on SF.net 858 days ago, I think
that tacg is abandonned and will not further try to package it.

https://sourceforge.net/tracker/?func=detail&aid=1874443&group_id=39048&atid=424133

-- 
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan

--- End Message ---
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