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[Genex-users] Re:
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From: Harry M. <hj...@ta...> - 2004-04-19 21:25:50
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This error is due to an unsubstituted variable (%%GENEX_PORT%%) making it thru
the substitution script. This should never happen. It's supposed to be
substituted to 5432 and replaced everywhere it occurs.
Hrishi - did you set up the DB to be TCP-available or just localhost? ie what is
the GENX_HOST line in your GeneX.config file?
teh localhost version would look like this:
'GENEX_HOST' => 'localhost',
Jason - have you seen this before? Is this a problem with making the pg DB
TCP-available instead of just localhost? I have to admit that I don't remember
making it TCP-available recently, but I'll check it out.
hjm
hde...@gm... wrote:
> Hi Harry,
>
> For the pg_nba.conf,was just a bit puzzled with IPs,one IP is for local host and the second is the the IP of the machine on which genex is being installed?!
> But i think i figured it out.
> I edited the GeneX.config file and was at make install step,i have already sent email about this,just incase you did not receive it (my skl's email is slow), here is the error which i encountered:
>
> Ok, this will take a few minutes, hit [Enter] to proceed.
>
> Perl/scripts/gendb.pl --db genex --dir /home/deshmuk/genex-server --user genex --pass xxxx --no_ecoli_sf
> Creating DB ...
> /usr/local/genex/bin/create-genex-db.pl --dbname genex --username genex --password hyde00 --rootdir /home/deshmuk/genex-server /home/deshmuk/genex-server/DB/xml/GENEX_ARRAY.xml /home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_DESIGN.xml /home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_MANUFACTURE.xml /home/deshmuk/genex-server/DB/xml/GENEX_AUDIT.xml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL.xml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_CHARACTERISTIC.xml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHANGELOG.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHROMOSOME.xml /home/deshmuk/genex-server/DB/xml/GENEX_CITATION.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTACT.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTROLLED_VOCAB.xml /home/deshmuk/genex-server/DB/xml/GENEX_
DATABASE.x.........................
> DBI connect('dbname=template1;host=wellerlab1.binf.gmu.edu;port=%%GENEX_PORT%%','genex',...) failed: could not connect to server: Connection refused at /usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm line 196
> Couldn't connect to template1: could not connect to server: Connection refused at /usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm line 201.
> Died at Perl/scripts/gendb.pl line 108.
>
> FATAL ERROR
>
> I got an error when I ran the DB installer.
>
>
> !! System Error: @ line: 341 (su -c '/usr/bin/perl /home/deshmuk/genex-server/Perl/scripts/db.pl' postgres)
>
> FATAL ERROR
>
> I got an error when I ran the DB installer.
>
> make: *** [install] Error 9
>
>
> Waiting for your reply.
>
> Thanks,
> Hrishi
>
>
>
>
>
>>Hi Hrishi,
>>
>>Good point of clarification.
>>
>>If you install postgres as per the apt-get line you mention in 1),
>>you should
>>not have to do much else, besides following the instructions in
>>the section marked:
>>
>>
>>Modify configuration files:
>>===========================
>>1- ...
>>
>>2 - modify the Postgresql config file for GeneX:
>>
>>which tells you how to modify the PG config file.
>>
>>The lines:
>>
>>> For the basic postgres installation, please see:
>>> http://www.postgresql.org/docs/7.4/interactive/installation.html
>>
>>point you to the documentation that tell you how to do the basic
>>postgres
>>installation. (You should understand the basics of how the system
>>works.)However the specifics are mentioned in the postgres stanza
>>
>>hde...@gm... wrote:
>>
>>>Hi Harry,
>>>
>>>Couple of "silly" questions:
>>>
>>>I have been following the instructions/guidelines given in the
>>
>>INSTALL documnet in the latest genex-server dir (did svn
>>.............)>
>>
>>>1) I did:
>>>The following commands pasted into a root shell will install
>>
>>most of
>>
>>>the pre-requisites you need to support GeneX :
>>>
>>>apt-get update
>>>
>>>apt-get install postgresql postgresql-dev postgresql-client
>>
>>postgresql-doc \
>>
>>> libpgtcl libpgperl pgaccess unixodbc-bin expat perlSGML apache-
>>
>>dev \
>>
>>> libapache-mod-perl libdevel-symdump-perl odbc-postgresql
>>
>>libpgjava \
>>
>>> perl-modules libterm-readkey-perl libapache-session-perl \
>>> libapache-request-perl libdbd-pg-perl libdbi-perl \
>>> libhtml-mason-perl libtie-ixhash-perl libxml-xerces-perl r-base-
>>
>>core \
>>
>>> r-recommended r-base r-base-dev r-base-html odbc-postgresql
>>
>>libiodbc2 \
>>
>>> unixodbc libpgjava pgaccess unixodbc-bin postgresql-client
>>
>>postgresql-doc \
>>
>>> libecpg-dev libpgtcl libdbd-pgsql
>>>
>>>Now the question is do i have to install postgresql , as per the
>>
>>instructions given @
>>
>>>2 - modify the Postgresql config file for GeneX:
>>>
>>> For the basic postgres installation, please see:
>>> http://www.postgresql.org/docs/7.4/interactive/installation.html
>>>
>>>OR does it mean that when i did step (1) postgresql was
>>
>>installed and i can skip the link and what it says??!!
>>
>>>Now at the step of enabling GeneX2 DB for remote access via TCP,
>>
>>one IP is the local host, the second IP should be the IP of the
>>machineon which genex is being installed?!
>>
>>The paragraph below that tells what the 2 numbers are:
>>
>>
>># TYPE DATABASE USER IP-ADDRESS IP-MASK
>>METHOD
>>host all all 127.0.0.1 255.255.255.255
>>password
>>host genex all 192.168.1.0 255.255.255.0
>>password
>>
>> In the above example, the first line allows all users from the
>>local machine
>> to access all databases as long as they provide valid
>>passwords. The second
>> line allows machines from a private subnet (192.168.1.0, masked
>> 255.255.255.0) to access only the genex DB and only if they
>>are known
>> postgres users and supply the correct postgresql password.
>>There are more
>> (and less) stringent authentication schemes described in the
>>comments in
>> 'pg_hba.conf'.
>> The two net address fields specify to which client machines a
>>host or
>> hostssl record applies, based on their IP address. The
>>precise logic
>> is that the (actual-IP-address XOR IP-address-field) AND IP-
>>mask-field must
>> be zero for the record to match.
>>
>>
>>>Trivial/silly, i thought it was good to clarify just in case and
>>
>>may be add a
>>line or two in the INSTALL doc that resolves these "silly" questions.
>>
>>what part of the above is unclear? Did you read the comments in
>>the pg_hba.conf
>>file? I admit, it's not drop-dead simple, but it's the way
>>postgres works and
>>if you don't understand the postgres basics, you won't be able to
>>administer the
>>system.
>>
>>
>>
>>>Waiting for your reply.
>>>
>>>Thanks,
>>>Hrishi
>>>
>>>
>>>
>>>
>>>
>>
>>--
>>Cheers, Harry
>>Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
>> <<plain text preferred>>
>>
>
>
>
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
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