Re: [GeneX-dev] Installation experience..

[Michael P. <mic...@ho...>]

>   # *Looking for xcluster in path, but executable by default  from stanford
>   # is cluster in xcluster directory.
>
> ?? I don't understand this. Could you rephrase?

My turn for confusing phrases... I meant that you are looking for
an xcluster executable file, but the executable file is named cluster that
results from the makefile that comes with the distribution from Stanford.

M. Pear

----- Original Message -----
From: "Harry Mangalam" <man...@ho...>
To: <gen...@li...>
Sent: Thursday, January 25, 2001 9:14 AM
Subject: Re: [GeneX-dev] Installation experience..


> Hi Michael,
>
> Can you tell Outlook to do text only mail?  Your mail come thru in a way that it doesn't get
picked up when I try to reply (anyone else have that problem?)
>
> Here are my comments on your (welcome) comments.  I have things just about cleared away so I can
help Jason patch / test these today..
>
> hjm
>
>
>   #
>   # Hi Jason,
>   #
>   # Here is some feedback regarding pre6...it is looking really good. There
>   # is only one problem that really should be addressed in your script:
>   # make sure that when an executable is supplied that it REALLY is an
>   # executable file instead of a directory.
>   #
>   # Other than that, many of the other things are fine tuning or
>   # documentation in the INSTALL doc.
>   #
>   # Great work! I know you'll be glad when this is over.
>   #
>   # Regards,
>   #
>   # Michael Pear
>   #
>   # -----------------------------------
>   #
>   # ****It is possible to enter a directory name as a substitute for an
>   # executable in the section asking program names, and it is particularly
>   # sticky once this is done. After installing dtd2html in my local
>   # directory not in the path, I accidentally entered /var/genex/local/bin
>   # without pointing all the way to the executable. After that, the only
>   # way I could recover was to edit the Bio/Genex/Config.pm file directly.
>   # Even when I ask to answer the installation questions again, it appears
>   # that it is checking the location of the executables rather than asking,
>   # so it keeps finding the directory. I think this is the most critical
>   # issue left in the installation, for those of us prone to making
>   # mistakes.
>
> OK - Adding a check for -f and -x would cure this, no?
>
>   # ***Perl modules are still one of the  most difficult to get right. I
>   # suggest you recommend XML::Parser and XML::DOM to make sure that parser
>   # works right before other tests. The problem with the XQL tests throws
>   # a wrinkle in because those problems are acceptable, but ones with the
>   # XML:Parser for example aren't. Harry noted that Class::ObjectTemplate
>   # isn't brought in automagically through dependency when installing
>   # Class::ObjectTemplate::DB, so you need to make those separate.
>
> And we should still automate this as much as possible.  I had volunteered
> to check into rolling the automatic install ofperl modules into the
> installation, bt I dropped the ball here.  We would have to careful about
> which modules were completely auto-installable and which had to be manually
> configured to ge the right params..
>
>   # **Rcluster queue_master gets mentioned, but I didn't need to start it
>   # before to get Rcluster to work....why not? ***Also, what happens on
>   # system reboot?
>
> The original rcluster installation code automatically started a
> queue-master regardless of how many were already running (so after several
> passes of installation tests I was running 15 copies).  Instead of fixing
> it at the time to detect this I  just commented out the code to allow me
> to fix what I was after.
>
> Jason remedied this but it still needs to be added to a genex init script,
> which DOES need to be installed as root in /etc/[rc.d]/init.d and
> symlinked into the appro startup.  Because the different Linux distro's
> put their scripts in different places, we could try to detect which distro
> (I think Jason already added this code) and put it in the appro place (or
> we could just write the script and have root install it where they want).
> The script will fail on Solaris unless we do some more testing, I think.
>
>   # **Installation itself completing  with no errors depends on dtd2html,
>   # it appears, so you might as well check earlier and kick things out if
>   # the it isn't installed.
>
> Also, looking at the .subst-cache on genomics I also noted that several
> apps were NOT detected (like sendmail below), but these errors
> were not caught at runtime or reported by the error reporting at the end.
>
>   # **Question reusing cached values vs. setting new values is confusing.
>   # Currently, the formatting always throws  me...I never quite know until
>   # I read the question several times what enter will do. I suggest
>   # changing this to a yes/no question with yes as default. "Enter/No"
>   # isn't really a common way people look at answering questions.
>
> Good point - there are a few of these inthe script - please tell us of
> others that seem oddly phrased (says the chief odd-phrase maker...).
>
>   # *Looks like all doc mods are made to INSTALL....README is out of date
>   # and probably should be removed or changed to refer installer to INSTALL
>   # file.
>
> Yes - I think both Jason and I have been adding to INSTALL.
>
>   # *Java dependency should be noted for Jpython. Jpythonc is part of
>   # Jpython1.1. Direct installer to look for JPython1.1 rather than
>   # jpythonc. It isn't clear what this is used for on the server, anyways.
>   # Can it be left out? I thought this was more of a development issue for
>   # the dendogram applet. (It will be nice to get rid of this in a future
>   # release, python may be a great scripting language, but you have plenty
>   # of languages to go around at the moment in GeneX!)
>
> My fault (being Java-ignorant, I thought the class file had to be built for
> each installation as APD has a jpythonc build line in his makefile).
> This should not be the case for the distro and in fact that line should be
> removed from the rcluster build if we're distibuting the class file (which
> we are, I think..)
>
>   # *Xgobi directory requested...why? Xgobi/xgvis are requested later on
>   # independent of this request. Also, it sort of throws me off in the flow
>   # because my first instinct when it asks for xgobi again is to enter a
>   # directory, not the executable.
>
> This is required to set the env variable XGOBID to point to the xgobi
> help files which are typically in a different place than the executables.
> If xgobi is installed in the genex directory, this could be more automated,
> but I thought it would be so variable that I'd ask for it.
>
>   # */usr/sbin/sendmail not detected, although it is a common location
>   # often not in  non-root user's path.
>
> Yup.  Hmmm.  It's typically on root's PATH, but not on users's....
> we could try a `locate bin/sendmail | wc, check to see if there's more than
> one and then ask which one it was if so...?  I'll play with this
>
>   # *Looking for xcluster in path, but executable by default  from stanford
>   # is cluster in xcluster directory.
>
> ?? I don't understand this. Could you rephrase?
>
>   # *Missed picking up existing tmp file definition in rerun of install.
>   # Most values are picked up and presented as defaults, but tmp file
>   # definition is not for some reason.
>
> ?!  Odd.  I'll check.
>
>
> --
> Cheers,
> Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
>
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