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seqpup: client-server at last...

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Tue Jul 2 09:16:58 EST 1996

Greg and others, I'll be happy to provide what advice I can
about setting up bopper and configuring it to use w/ GCG or
other biocomputing software, and likewise for setting up seqpup
for new services.

On the server side is a small network daemon which listens on
a port# (7110 default) and talks this BOP language w/ seqpup.
To configure the server, there is a config. file that includes
lines like
app     map     /usr/local/bin/bopgcg map
(1)     (2)       (3)                 (4+)

item 1 = config section.  use 'app' for a new application
item 2 = name used by client.  anything you want, so long as client uses it
item 3 = path to executable
item 4 = any command line parameters, to add *before* client command line

Other bopper.conf config sections are not yet important.

The program 'bopgcg' is a shell script that sets environment then
calls the appropriate gcg routine.  Its main function is
  exec $* -default
meaning all command line parameters are executed, and "-default" is
tagged on at the end to prevent gcg programs from asking questions.

On the client side, you want to create a dialog in HTML form style
(not all HTML form tags are fully supported yet, but basic ones are).
There are various hidden tags you would use to specify input and output
data files that SeqPup knows about.

Once you create an appropriate HTML form, installing it for SEqPup use
requires editting "SeqPup.prefs" with a new version number, &/or editing
the system specific 'seqpup.cnf' or 'seqpup.ini' or '.seqpuprc' config
file.  In SeqPup.prefs, see the section

bop_title=[BOP servers]
gcg_map=GCG Map...
gcg_blast=GCG Blast...

which lists menu titles, then also a following section for each
new entry such as


Here is an abbreviated gcg_map.html form
Note the special variables ($bophost, $bopport), variables defined
as dialog checkboxes and such ($menu, $three $silent $perfect)
that correspond to gcg map command line options.

<title>GCG Map</title>
<b>GCG Map</b> - Restriction and other mapping of sequence 
by Genetics Computer Group
	myseq -OUT=myseq.map -MEN=$menu 
	$three  $silent $perfect $all $six $once
<INPUT TYPE=submit VALUE="Launch app"> 
Program options:<p>
Translation frame:
<OPTION VALUE=s>"six frames"
<OPTION VALUE=t>"three frames"
<OPTION VALUE=o>"open reading frames"
<INPUT TYPE="checkbox" NAME=six VALUE="-SIX">
Find only enzymes with 6 or more bases in recognition site.
<INPUT TYPE="checkbox" NAME=once VALUE="-ONC">
Show only enzymes that cut once.
<!-- more options here --->
Other options: <p>

<INPUT TYPE=hidden NAME=infile VALUE="myseq">
<INPUT TYPE=hidden NAME=seqformat VALUE="gcg">
<INPUT TYPE=hidden NAME=minseq VALUE="1">
<INPUT TYPE=hidden NAME=maxseq VALUE="1">
<INPUT TYPE=hidden NAME=outfile1 VALUE="myseq.map  text/plain">

my documentation always lags the software and is minimal or lacking
... mainly it takes more time than I have to make this complex
a collection of software avaiable in a good package.  But next
revision may be better :)   
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu

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