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[GeneX-dev] Re: [Genex-users] Re:
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From: Harry M. <hj...@ta...> - 2004-04-19 22:57:31
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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:
>>>>>>>
>>
>>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>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>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
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>>>>_______________________________________________
>>>>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>>
|
