Re: [Gmod-gbrowse] OSX probems

[Todd H. <ha...@cs...>]

Hi Bob - 

I seriously recommend building everything from source and avoiding fink.
I'm guessing that since you have GBrowse 1.54a installed that you used the
package.

I can build all requirements for GBrowse on Mac OS X - including things like
mysql, apache, and mod_perl in under an hour.  This includes the bottleneck
of network fetching.  If your sysadmin is interested, have her contact me
and I can pass along a script that does this.  It's not ready for
prime-time, but I'd appreciate your beta testing.

Todd


===================================
Todd W. Harris, PhD
Stein Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724 USA
ph 801-971-5434
===================================


> On 11/23/04 12:44 PM, Bob Sinclair wrote:

> This may have a connection to the messages in digest Vol 1 #403, and Todd's
> response to Josh's questions that the OSX packages may not be all they
> could be.
> 
> We have also installed GBrowse on a Mac as a pilot project for putting it
> on a Sun440 system. The components we have are
> Mac G5 Dual 2.0GHz with 8GB of ram.
> OSX 10.3.6
> BioPerl 2.1.5
> GBrowse 1.54a
> Perl 5.8.1
> and 2 Myql folders: -max-4.0.14-apple-darwin6.4-powerpc and
> -standard-4.0.21-apple-darwin7.5.0-powerpc.
> 
> Running Gbrowse from the flatfiles all seems to work fine. All the tutorial
> stuff went well and we were able to create some mouse tracks.(However, as
> expected a fairly minimal transcript set for the mouse grinds the system to
> a halt despite lots of memory.)
> 
> When we try to get the mySQL part running we run into all manner of
> difficulties. The SysAd who did the installation attempted to install
> everything according to the directions, but I run into several problems.
> 
> First of all, mysql doesn't seem to be in any path. mysql from any command
> prompt gives a command not found error, even run from right in the
> mysql.../bin folder (but running from this folder using ./mysql launches it
> fine.). "which mysql" fails to find an executable in the environment, but
> the lack of ability to "run it from it's location" suggests the mysql
> command is pointed elsewhere. Both versions of mysql on the machine seem to
> access the same database space, BTW, as a db created in one place is
> visible from a mysql instance run from the other.
> 
> Second, while the SysAd is sure it installed, bp_load_gff.pl doesn't seem
> to be present anywhere on the system - either searched using "which" or
> using finder.
> 
> I am sure we have some read-write permission issues that may be
> contributing. It seems likely that some link/environment/?? parameters have
> been incorrectly set up (or not set up at all). Before we start tearing it
> all apart and redoing stuff do you have any suggestions for things we
> should look at or try?
> 
> One thing that I did notice is that during the install, a folder was set up
> called BoiTeamInfxInstallers -- this looks like it should be "Bio..." not
> "Boi..." so is it possible that a subsequent script has been looking for
> components in the wrong place?
> 
> Any help on any of this will be hugely appreciated,
> 
> On the Sun side of the coin, the SysAd there tells me he's having all
> manner of problems with GD. He's out this week, so I can't get an update,
> but if there are any known tricks to getting that up and running we'd
> appreciate a pointer.
> 
> Thanks,
> 
> Bob.
> 
> 
> 
> 
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