[GeneX-dev] Installation experience..

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

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.

***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.

**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?=20

**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.

**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.

*Looks like all doc mods are made to INSTALL..README is out of date and =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.

*-init-dump.pl assumes write permissions for the postgres user to the =
install database so that init-dump.pl can be created. Perhaps should be =
noted  in instructions, or can init-dump.pl be created in a tmp location =
and used from there? Any other things written?

*Readonly and genex passwords password not masked on entry he first =
time. The genex password is requested later on and it is masked and =
verified. Does it need to ask twice?

*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!)

*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.=20

*/usr/sbin/sendmail not detected, although it is a common location often =
not in  non-root user's path.

*Looking for xcluster in path, but executable by default  from stanford =
is cluster in xcluster directory.

*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.=20

=20