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[Genex-users] Re: Re:
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From: <hde...@gm...> - 2004-04-19 20:46:47
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Hi Harry,
For the pg_nba.conf,was just a bit puzzled with IPs,one IP is for loc=
al host and the second is the the IP of the machine on which genex is=
being installed?!=20
But i think i figured it out.
I edited the GeneX.config file and was at make install step,i have al=
ready sent email about this,just incase you did not receive it (my sk=
l'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 --u=
ser genex --pass hyde00 --no_ecoli_sf
Creating DB ...
/usr/local/genex/bin/create-genex-db.pl --dbname genex --user=
name genex --password hyde00 --rootdir /home/deshmuk/genex-server /ho=
me/deshmuk/genex-server/DB/xml/GENEX_ARRAY.xml /home/deshmuk/genex-se=
rver/DB/xml/GENEX_ARRAY_DESIGN.xml /home/deshmuk/genex-server/DB/xml/=
GENEX_ARRAY_MANUFACTURE.xml /home/deshmuk/genex-server/DB/xml/GENEX_A=
UDIT.xml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL.xml /hom=
e/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_CHARACTERISTIC.xml /h=
ome/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_LINK.xml /home/desh=
muk/genex-server/DB/xml/GENEX_CHANGELOG.xml /home/deshmuk/genex-serve=
r/DB/xml/GENEX_CHROMOSOME.xml /home/deshmuk/genex-server/DB/xml/GENEX=
_CITATION.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUE=
NCE.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE_LI=
NK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTACT.xml /home/desh=
muk/genex-server/DB/xml/GENEX_CONTROLLED_VOCAB.xml /home/deshmuk/gene=
x-server/DB/xml/GENEX_DATABASE.x.........................
DBI connect('dbname=3Dtemplate1;host=3Dwellerlab1.binf.gmu.edu;port=
=3D%%GENEX_PORT%%','genex',...) failed: could not connect to server: =
Connection refused at /usr/local/share/perl/5.8.3/Class/ObjectTemplat=
e/DB/Connect.pm line 196
Couldn't connect to template1: could not connect to server: Connectio=
n refused at /usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Conn=
ect.pm line 201.
Died at Perl/scripts/gendb.pl line 108.
FATAL ERROR
I got an error when I ran the DB installer.=20
!! System Error: @ line: 341 (su -c '/usr/bin/perl /home/deshmuk/ge=
nex-server/Perl/scripts/db.pl' postgres)
FATAL ERROR
I got an error when I ran the DB installer.=20
make: *** [install] Error 9
Waiting for your reply.
Thanks,
Hrishi
> Hi Hrishi,
>=20
> Good point of clarification.
>=20
> If you install postgres as per the apt-get line you mention in 1),=
=20
> you should=20
> not have to do much else, besides following the instructions in=
=20
> the section marked:
>=20
>=20
> Modify configuration files:
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D
> 1- ...
>=20
> 2 - modify the Postgresql config file for GeneX:
>=20
> which tells you how to modify the PG config file.
>=20
> The lines:
> > For the basic postgres installation, please see:
> > http://www.postgresql.org/docs/7.4/interactive/installation.ht=
ml
>=20
> point you to the documentation that tell you how to do the basic=
=20
> postgres=20
> installation. (You should understand the basics of how the system=
=20
> works.)However the specifics are mentioned in the postgres stanza
>=20
> hde...@gm... wrote:
> > Hi Harry,
> >=20
> > Couple of "silly" questions:
> >=20
> > I have been following the instructions/guidelines given in the=
=20
> INSTALL documnet in the latest genex-server dir (did svn=20
> .............)>=20
> > 1) I did:
> > The following commands pasted into a root shell will install=20
> most of=20
> > the pre-requisites you need to support GeneX :
> >=20
> > apt-get update
> >=20
> > apt-get install postgresql postgresql-dev postgresql-client=20
> postgresql-doc \
> > libpgtcl libpgperl pgaccess unixodbc-bin expat perlSGML apache-
> dev \
> > libapache-mod-perl libdevel-symdump-perl odbc-postgresql=20
> 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=20
> libiodbc2 \
> > unixodbc libpgjava pgaccess unixodbc-bin postgresql-client=20
> postgresql-doc \
> > libecpg-dev libpgtcl libdbd-pgsql=20
> >=20
> > Now the question is do i have to install postgresql , as per the=
=20
> instructions given @
> > 2 - modify the Postgresql config file for GeneX:
> >=20
> > For the basic postgres installation, please see:
> > http://www.postgresql.org/docs/7.4/interactive/installation.ht=
ml
> >=20
> > OR does it mean that when i did step (1) postgresql was=20
> installed and i can skip the link and what it says??!!
> >=20
> > Now at the step of enabling GeneX2 DB for remote access via TCP,=
=20
> one IP is the local host, the second IP should be the IP of the=
=20
> machineon which genex is being installed?!
>=20
> The paragraph below that tells what the 2 numbers are:
>=20
>=20
> # TYPE DATABASE USER IP-ADDRESS IP-MASK =
=20
> METHOD
> host all all 127.0.0.1 255.255.255.255 =
=20
> password
> host genex all 192.168.1.0 255.255.255.0 =
=20
> password
>=20
> In the above example, the first line allows all users from the=
=20
> local machine
> to access all databases as long as they provide valid=20
> 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=20
> are known
> postgres users and supply the correct postgresql password. =
=20
> There are more
> (and less) stringent authentication schemes described in the=
=20
> comments in
> 'pg_hba.conf'.
> The two net address fields specify to which client machines a=
=20
> host or
> hostssl record applies, based on their IP address. The=20
> precise logic
> is that the (actual-IP-address XOR IP-address-field) AND IP-
> mask-field must
> be zero for the record to match.
>=20
> >=20
> > Trivial/silly, i thought it was good to clarify just in case and=
=20
> may be add a=20
> line or two in the INSTALL doc that resolves these "silly" question=
s.
>=20
> what part of the above is unclear? Did you read the comments in=
=20
> the pg_hba.conf=20
> file? I admit, it's not drop-dead simple, but it's the way=20
> postgres works and=20
> if you don't understand the postgres basics, you won't be able to=
=20
> administer the=20
> system.
>=20
>=20
> >=20
> > Waiting for your reply.
> >=20
> > Thanks,
> > Hrishi
> >=20
> >=20
> >=20
> >=20
> >=20
>=20
> --=20
> Cheers, Harry
> Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
> <<plain text preferred>>
>=20
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