From mwilkinson@gene.pbi.nrc.ca Fri May 10 15:50:01 2002 From: mwilkinson@gene.pbi.nrc.ca (Mark Wilkinson) Date: Fri, 10 May 2002 08:50:01 -0600 Subject: [Genquire-users] Blast_vs_EST table to be deprecated References: <3CC58428.F2079829@illuminae.com> Message-ID: <3CDBDE19.7F113B6F@gene.pbi.nrc.ca> Hello Genquire users and developers, I am planning to deprecate the database table Blast_vs_EST in the next release of Genquire. I removed the GUI elements that called on that table quite some time ago, so I am guessing that none of you are using it. It seems more sensible, now, for EST 'hits' to be mapped as features (using the standard Feature table), and a plugin can then be used to see more detailed alignments if that is needed. Having said that, I will probably resurrect the SIM4 viewer as a plugin before the next release as well... If this is going to cause anyone any big headaches let me know. Cheers! Mark -- -------------------------------- "Speed is subsittute fo accurancy." ________________________________ Dr. Mark Wilkinson Bioinformatics Group National Research Council of Canada Plant Biotechnology Institute 110 Gymnasium Place Saskatoon, SK Canada From mwilkinson@gene.pbi.nrc.ca Tue May 14 18:58:11 2002 From: mwilkinson@gene.pbi.nrc.ca (Mark Wilkinson) Date: Tue, 14 May 2002 11:58:11 -0600 Subject: [Genquire-users] Genquire under OS X Message-ID: <3CE15033.31F65D15@gene.pbi.nrc.ca> This is a multi-part message in MIME format. --------------5D7533DBB3C5BF5A7BB43E97 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'm sending this out just to get it into the archives so that people having problems will find it. The default "make" for Tk does not work under OS X. Some tweaking is required. As such, Genquire must be installed by hand on a Mac. look at the modules.conf file in the installer package for a list of the required CPAN modules you need to install. Attached is a description of how to install Tk on a Mac. M -- -------------------------------- "Speed is subsittute fo accurancy." ________________________________ Dr. Mark Wilkinson Bioinformatics Group National Research Council of Canada Plant Biotechnology Institute 110 Gymnasium Place Saskatoon, SK Canada --------------5D7533DBB3C5BF5A7BB43E97 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Mozilla-Status2: 00000000 Message-ID: <3CAC9F5F.D4FDDDA0@gene.pbi.nrc.ca> Date: Thu, 04 Apr 2002 12:45:51 -0600 From: Mark Wilkinson Organization: PBI-NRC X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.19 i686) X-Accept-Language: en MIME-Version: 1.0 To: dblock@gnf.org Subject: Bug's MacIntosh Page Content-Type: multipart/mixed; boundary="------------B7B8F8F79F3C59597EF236C2" This is a multi-part message in MIME format. --------------B7B8F8F79F3C59597EF236C2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit http://www.Lehigh.EDU/~sol0/Macintosh/X/ptk/ -- -------------------------------- "Speed is subsittute fo accurancy." ________________________________ Dr. Mark Wilkinson Bioinformatics Group National Research Council of Canada Plant Biotechnology Institute 110 Gymnasium Place Saskatoon, SK Canada --------------B7B8F8F79F3C59597EF236C2 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Base: "http://www.Lehigh.EDU/~sol0/Macintosh/ X/ptk/" Content-Location: "http://www.Lehigh.EDU/~sol0/Macintosh/ X/ptk/" Bug's MacIntosh Page

Perl/Tk and Mac OS X

The 10.2.1 release of Mac OS X seems to have introduced a compiler optimization bug that causes Perl/Tk to crash with bus errors and segmentation faults. The Perl that comes with Mac OS X, 5.6.0, is compiled with -O3, and that's what Perl/Tk uses, but we want to compile with no optimization. Many thanks to Richard Michaud for the heads-up and helping me track this down. So, here's the recipe for building a working Perl/Tk on Mac OS X:

That's it. Have fun, and remember to use Tk; --------------B7B8F8F79F3C59597EF236C2-- --------------5D7533DBB3C5BF5A7BB43E97--