[Genquire-dev] Improving the installer to be more self-sufficient on Linux?

[mwilkinson@gene.pbi.nrc.ca]

That's great!  thanks Danny!  I'll try it on my system this afternoon.

hey, have you noticed (have you used?) the TIGR BACS  recently?  I don't know
if this is a new problem, or an old one...  I tried running our
parse_bulk_contigs.pl script (in the Admin folder of genquire) over the
current set of TIGR Arabidopsis BACS, and it seemed to run quite happily, but
when I opened up the database in genquire it had successfully parsed
chromosomes 1, 2, and 3, but 4 and 5 were a complete nightmare, with many
contigs lacking a 5' end start position!  UGH!

Did you notice this when you parsed them last time? Is it a problem with our
parser, or a problem with their data?

I'm going to have a look at it early next week, but if you already know the
answer please clue me in :-)

I think there is also still something missing from the init_db routine...
Matt used it last week and found that it wasn't filling in some necessary
database fields during initialization.  I'll have a look at that too, as
these things MUST be fixed before the paper comes out in a few weeks.

Cheers!

M


Danny Yoo wrote:

> Hi everyone,
>
> I noticed that the Genquire installer on Linux prompts the user to press
> enter every so often for CVS interactively.  This is something of a
> hassle, but we can fix this by using the 'expect' utility.  'expect' is a
> tcl system that simulates keyboard input, so we can use it to type out
> 'cvs' or press enter on CVS password queries.
>
> Here's an expect script that enters in passwords for us:
>
> ######
> #!/usr/bin/expect
>
> ## Allow CVS commands to be run noninteractively.
> ## Parameters:  [password] [rest of cvs args]
> set password [lindex $argv 0]
> set cvsargs [lrange $argv 1 end]
> set password_wait 10
>
> set prompt "(%|#|\\$) $"          ;# default prompt
> catch {set prompt $env(EXPECT_PROMPT)}
> spawn $env(SHELL)
>
> ## If a password request comes within $password_wait seconds, we
> ## enter it in automatically.
> send -- "cvs -d $cvsargs\n"
> expect -timeout $password_wait -re "word: " {
>     send "$password\n"
> }
>
> expect  -timeout -1 -re $prompt
> send_user "\n"
> ######
>
> I've added this script into cvs as 'Installer/cvswrapper.sh'; we should be
> able to use it with Installer.pl so that the Linux installation goes as
> smoothly as the one on Windows.  Can you test it out on your systems?
>
> Hope this helps!
>
> _______________________________________________
> Genquire-dev maillist  -  Genquire-dev@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/genquire-dev

--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson, RA Bioinformatics
National Research Council, Plant Biotechnology Institute
110 Gymnasium Place, Saskatoon, SK, Canada

phone : (306) 975 5279
pager : (306) 934 2322
mobile: markw_mobile@illuminae.com