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Re: [Genex-users] Re:
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From: <hde...@gm...> - 2004-04-19 23:36:39
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Harry,
I did install bioperl but the same error, is there a Bio/Mage.pm from MGED or something that its searching for!!!!
Hrishi
____________________________________________________________________
'Life's battles don't always go to the stronger or faster man. But sooner or later the man who wins is the one who thinks he can.'
-Walter D. Wintle
----- Original Message -----
From: Harry Mangalam <hj...@ta...>
Date: Monday, April 19, 2004 6:57 pm
Subject: Re: [Genex-users] Re:
> Hi Hrishi,
>
> please write to the dev list. otherwise no one else will be able
> to benefit
> from your questions.
>
>
> hde...@gm... wrote:
> > Harry,
> >
> > I did modify the pg_hba.conf file,i put the configuration as
> suggested by the INSTALL
>
> doc at the end of the file but i guess it has to be at the "Put
> you
> configuration here" line.
>
> I don't follow what the above bit means. YOu can put it anywhere,
> but if
> there'a a later config line that contradicts or modifies its
> impact, it will
> take teh later one.
>
>
> > Do i need to install Bio-Perl!!!!
>
> Apparently. Don't for get to do a make configure each time before
> you run make
> install.
>
> > Its just set for localhost and here is the new error i am getting:
> > Finished
> > Finished
> > Adding mas5-short QuantitationTypeDimension ...
> > /usr/local/genex/bin/qtdim-insert.pl --dbname genex --
> username genex --password hyde00 /home/deshmuk/genex-
> server/DB/curated_data/qtdim-mas5-short.xml --name=MAS-short --
> abbrev_name=dmas5s --version=5.0 --feat="0" --
> data_start_regex1=^\s+ --data_end_regex=^$
> > Can't locate Bio/MAGE.pm in @INC (@INC contains: /etc/perl
> /usr/local/lib/perl/5.8.3 /usr/local/share/perl/5.8.3
> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8
> /usr/share/perl/5.8 /usr/local/lib/site_perl .) at
> /usr/local/genex/bin/qtdim-insert.pl line 14.
> > BEGIN failed--compilation aborted at /usr/local/genex/bin/qtdim-
> insert.pl line 14.
> > Died at Perl/scripts/gendb.pl line 226.
> >
> > 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
> >
> >
> > Thx,
> > Hrishi
> >
> >
> >
> >
> >>did you modify the pg_hba.conf file? Looks like you didn't.
> >>
> >>hjm
> >>
> >>
> >>hde...@gm... wrote:
> >>
> >>>Harry,
> >>>
> >>>Here is the error when i edit .config file for just localhost.
> >>>
> >>>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 --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','genex',...) failed: FATAL:
> >>
> >>IDENT authentication failed for user "genex" at
> >>/usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm
> line 196
> >>
> >>>Couldn't connect to template1: FATAL: IDENT authentication
> >>
> >>failed for user "genex" 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
> >>>
> >>>
> >>>AND
> >>>
> >>>Here is the errors from install-errors.txt
> >>>!! System Error: No such file or directory @ line: 266 (cp
> >>
> >>Mason/workspace/edit/species-edit.html
> >>/var/www/genex/mason/workspace/edit)>
> >>
> >>>!! System Error: @ line: 341 (su -c '/usr/bin/perl
> >>
> >>/home/deshmuk/genex-server/Perl/scripts/db.pl' postgres)
> >>
> >>>
> >>>
> >>>Thx,
> >>>Hrishi
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>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:
> >>>>>>>
> >>
> >>>>>"
> target="l">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:
> >>>>>>>
> >>
> >>>>>>"
> target="l">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>>
> >>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>Free Linux tutorial presented by Daniel Robbins, President and
> >>
> >>CEO of
> >>
> >>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>_______________________________________________
> >>>>Genex-users mailing list
> >>>>Gen...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/genex-users
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>--
> >>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>>
>
>
|
