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From: <ja...@op...> - 2004-08-11 01:49:55
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Hrishikesh Deshmukh <hde...@gm...> writes: > I have gone through the dev-list for the month of May and could not > find the email about the files and the mapping of the names. > Could you please forward the email from the list, i am unable to locate it. Sorry Hrishi my bad, it was April 27: https://sourceforge.net/mailarchive/message.php?msg_id=8244918 Cheers, jas. |
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From: <ja...@op...> - 2004-08-11 01:36:10
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Hrishikesh Deshmukh <gen...@ya...> writes: > Where do i find these scripts?! Hey Hrishi, (I've Cc:ed the genex-users list since this is probably the best place to archive the discussion) These files all live in the genex_server distribution in the DB/curated_data/ directory. Cheers, jas. > Hrishi > > "Jason E. Stewart" <ja...@op...> wrote: > Hrishikesh Deshmukh writes: > >> Yes in deed thats the last line in the file but what does it mean >> and how do i fix it! > > Hey Hrishi, > > Did this happen after we talked? If so, this is what I meant by > needing to rewrite fix-array.pl for each type of input file. It is set > up to only handle quantarray data files for input. You'll notice there > are 5 different scripts: > > * fix-array-cel.pl - .cel file input > * fix-array-mas4.pl - mas4 input > * fix-array-mas5.pl - mas5 input > * fix-array.pl - quantarray input > * fix-array-qa.pl - yet another version of quantarray input > > You should probably look at the other ones, they are most recent - the > original fix-array.pl was for mangling the probe names in one of > Karen's original data files. > > There are two ways to fix this: > 1) put a sample input file on genex2 and tell me where to find it so I > can write a script to handle it > 2) read the comments in the script to understand what the program > does, and modify it to work with your input. > > This are very simple scripts. All it does is go through every line of > the input file and writes out a simplified version that only has the > necessary pieces. The script needs to know: > 1) when to start reading in the spot data (that's what the two perl > regular expressions $data_start_regexp and $reading_data_regexp are > for > 2) what data columns to keep in the output file > 3) how to create a unique spot_identifier for each row of data. Affy > files have a unique probe name, quantarry files use a concatenation > of the four values: row, column, grid_row, and grid_column. > > Requiring ArrayDesign's is a *painful* part of data loading - but this > is something that only curators should ever have to do. It is needed > by the system because we have to map every expression value in the > data table to a spot on a chip - and to do that we need a uniform way > of creating spot_identifiers. > > If someone comes up with a better approach I will be forever grateful. > > Cheers, > jas. > >> Harry Mangalam wrote: >> Hi Hrishi, >> >> That's a strange place for genex to be installed - I don't remember installing >> it at root, tho I may be mistaken. >> >> Also, it's an odd error - there is no '==' at line 230 - I'm assuming it's the >> one that finished the stanza at 232. >> >> I think this implies that the input is at line 3195 - is that the end of the >> file or does that line look peculiar in any way relative to the rest of the file? >> >> >> >> Hrishikesh Deshmukh wrote: >>> Hi All, >>> >>> Here is the error which i get when i try to run fix-array.pl script on a >>> cDNA file. >>> >>> $ perl /genex/bin/fix-array.pl --in mssm.txt --design /tmp/mssm_fix.txt >>> Use of uninitialized value in numeric eq (==) at /genex/bin/fix-array.pl >>> line 230, line 3195. >>> Finished >>> Thanks, >>> Hrishi >>> >>> ------------------------------------------------------------------------ >>> Do you Yahoo!? >>> Yahoo! Mail Address AutoComplete >>> >>> - You start. We finish. >> >> -- >> Cheers, Harry >> Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta... >> < >>> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media >> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 >> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. >> http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 >> _______________________________________________ >> Genex-dev mailing list >> Gen...@li... >> https://lists.sourceforge.net/lists/listinfo/genex-dev >> >> __________________________________________________ >> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best spam protection around >> http://mail.yahoo.com > > > ------------------------------------------------------- > SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media > 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 > Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. > http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev > > > --------------------------------- > Do you Yahoo!? > Yahoo! Mail - 50x more storage than other providers! |
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From: <ben...@id...> - 2004-05-25 08:34:37
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Dear Open Source developer I am doing a research project on "Fun and Software Development" in which I kindly invite you to participate. You will find the online survey under http://fasd.ethz.ch/qsf/. The questionnaire consists of 53 questions and you will need about 15 minutes to complete it. With the FASD project (Fun and Software Development) we want to define the motivational significance of fun when software developers decide to engage in Open Source projects. What is special about our research project is that a similar survey is planned with software developers in commercial firms. This procedure allows the immediate comparison between the involved individuals and the conditions of production of these two development models. Thus we hope to obtain substantial new insights to the phenomenon of Open Source Development. With many thanks for your participation, Benno Luthiger PS: The results of the survey will be published under http://www.isu.unizh.ch/fuehrung/blprojects/FASD/. We have set up the mailing list fa...@we... for this study. Please see http://fasd.ethz.ch/qsf/mailinglist_en.html for registration to this mailing list. _______________________________________________________________________ Benno Luthiger Swiss Federal Institute of Technology Zurich 8092 Zurich Mail: benno.luthiger(at)id.ethz.ch _______________________________________________________________________ |
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From: <hde...@gm...> - 2004-05-04 15:52:48
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Yeah,I can do that,just helped my friend load Fedora and now that i have a Fedora system to play with..... Will doc everything.There are few things right now that will keep me busy but will give it a shot ASAP. Thx, 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: Tuesday, May 4, 2004 11:31 am Subject: [Genex-users] Re: > Not for a while (on RH anyway). You want to try it? If you do, > doc everything. > > hjm > > > hde...@gm... wrote: > > Hi Harry, > > > > Just curious can/did somebody try getting GeneX to work on > Fedora :)) > > > > Thanks > > Hrishi > > > > > > > > -- > Cheers, Harry > Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... > <<plain text preferred>> > > > ------------------------------------------------------- > This SF.Net email is sponsored by: Oracle 10g > Get certified on the hottest thing ever to hit the market... > Oracle 10g. > Take an Oracle 10g class now, and we'll give you the exam FREE. > http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click > _______________________________________________ > Genex-users mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-users > > |
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From: Harry M. <hj...@ta...> - 2004-05-04 15:32:37
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Not for a while (on RH anyway). You want to try it? If you do, doc everything.
hjm
hde...@gm... wrote:
> Hi Harry,
>
> Just curious can/did somebody try getting GeneX to work on Fedora :))
>
> Thanks
> Hrishi
>
>
>
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
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From: <hde...@gm...> - 2004-05-04 13:26:11
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Hi Harry, Just curious can/did somebody try getting GeneX to work on Fedora :)) Thanks Hrishi |
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From: <ja...@op...> - 2004-05-04 04:42:12
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kad...@gm... writes: > Why does the link say nologin ??? > > Whew!! Time to point your browser at: > > http://wellerlab2.binf.gmu.edu/genex/mason/nologin/docs/docs.html > and give it a whirl. Because that is what the URL is now - I had to break off the pieces into 'login' and 'nologin' because the login stuff requires a DB account to access, and the nologin stuff does not. Cheers, jas. |
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From: <ja...@op...> - 2004-04-21 17:37:40
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Hey All, To ensure getting a proper update please do the following *before* running 'svn update': $ rm -rf Perl/scripts/ $ rm -rf Mason $ svn update and you will have a working set of source code. I repeat: if you do not remove the Perl/scripts and Mason directories, you will get an svn error and you will have a broken source code distribution. The reason for this is that I've removed all the old unnecessary .in files from the distribution, and so there are name clashes. You can either checkout a new version (which is more work), or you can remove the files that clash like I suggested above. My appologies for doing this in the middle of your working time - but just as I was committing my work I lost my internet connection after I had committed half the files and it just came back. Again my appologies, but all should be stable at this point. Thanks for bearing with me. Cheers, jas. |
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From: <ja...@op...> - 2004-04-21 17:04:46
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ja...@op... (Jason E. Stewart) writes: > kad...@gm... writes: > > > kaddepal@1[genex-server]$ svn update > > svn: Failed to add file 'Perl/scripts/create-db-roles.pl': object of the same name already exists > > kaddepal@1[genex-server]$ > > Did you not see my email warning about this? I'm shifting things > around in SVN. Please read my email on genex-dev and redo the SVN > update - your working copy is broken. Sorry, just in case it didn't come through, here is the message I sent earlier. If you ever do an 'svn update' and it returns: 'Failed' - something is very bad and you should fix it. Cheers, jas. ja...@op... (Jason E. Stewart) writes: > ja...@op... (Jason E. Stewart) writes: > > > I'm checking in some unstable code for testing on genex2 - please > > don't commit or update for another 10 minutes or so until I mail the > > list again. > > OK. > > I've moved all .pl.in files in the Perl/scripts directory to be just > plain old .pl files. SVN will complain if you attempt to do an update > because the old .pl files will be in the way so do this: > > $ rm Perl/scripts/* > $ svn update > > and everthing should be fine. > > I've made all substitution parameters in the .pl files be runtime > calls to Config.pm and they all use /usr/bin/perl in the shebang > line. I added code to Install that checks if the install is using > /usr/bin/perl and if so, just copy all .pl files to their installation > directory as-is. If using a different interpreter then modify the > shebang line during the copy. > > This way all Perl scripts are usable as is without needing to do a > 'make substitute' - this is a big headache removed for us developers > (me??) - who was far too often editing the .pl file instead of the > .pl.in file and losing his changes on the next 'make substitute'. > > My next target are all the .in files in the Mason directory. > > Cheers, > jas. > > > ------------------------------------------------------- > 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-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: <ja...@op...> - 2004-04-21 16:51:42
|
kad...@gm... writes: > kaddepal@1[genex-server]$ svn update > svn: Failed to add file 'Perl/scripts/create-db-roles.pl': object of the same name already exists > kaddepal@1[genex-server]$ Did you not see my email warning about this? I'm shifting things around in SVN. Please read my email on genex-dev and redo the SVN update - your working copy is broken. Cheers, jas. |
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From: Harry M. <hj...@ta...> - 2004-04-21 16:03:48
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kad...@gm... wrote:
> Hi Harry and Jason,
> Here is what it today morning from the beginning :
>
> As Root:
> I changed my pg_hba.conf file according to Harry's file.
> I also changed the LOCAL_DIR , in GeneX.conf file to point to "/user/local"
Did you edit it to be "/user/local" or "/usr/local" ?
If the former, then of course the genex.conf file is in /user/local/
^^^^
not /usr/local and your apache conf file has to be pointed to the right place.
Hmmm - from the errors, it looks like you set the LOCAL_DIR to be:
user/local (missing the leading '/') - is that the case?
The errors from the file install-errors are mistakes deriving from extra lines
from the MANIFEST file - I'm waiting for Jason's input before I clear them up.
hjm
> then :
> As User :kaddepal
> $ svn update
> $ make configure
> and then again as root:
> make install
>
> Errors:
> when I did svn update :
>
> kaddepal@1[genex-server]$ svn update
> svn: Failed to add file 'Perl/scripts/create-db-roles.pl': object of the same name already exists
> kaddepal@1[genex-server]$
>
> I continued.
>
> after make install :
>
>
> Finished
>
> Congratulations! You have successfully installed the DB into Postgres.
>
>
>
> Changing permissions on Genex trees..
>
> You will need to add the following piece to your Apache config
> file:
>
> Include usr/local/genex/etc/genex.conf
>
> And restart the apache server.
>
>
>
> Whew!! Time to point your browser at:
>
> http://wellerlab2.binf.gmu.edu/genex/mason/nologin/docs/docs.html
>
> and give it a whirl.
>
> NB: If you haven't done so in a previous installation, you still have to:
> 1) add the text from the file [cron.entries] to the appropriate crontab
>
>
> ===========================================================================
>
> #### ERRORS WERE ENCOUNTERED ####
>
> There were errors in your installation. Please check the file
> [install-errors.txt] to see more information.
>
> Thank you!
>
> Then I added the line " Include usr/local/genex/etc/genex.conf " to httpd.conf file in the Apache folder.
>
> and then restarted apache.
>
> root@1[apache]# /etc/init.d/apache restart
> Configuration syntax error detected. Not reloading.
>
> [Wed Apr 21 11:14:53 2004] [warn] module perl_module is already loaded, skipping
> fopen: No such file or directory
> apache: could not open document config file /usr/local/genex/etc/genex.conf
> root@1[apache]#
>
>
> Install-errors.txt :
>
> !! System Error: No such file or directory @ line: 263 (cp
>
> Mason/comps/autohandler-top.mason
>
> !! System Error: No such file or directory @ line: 263 (cp
>
> Mason/comps/autohandler-bottom.mas
> ~
>
> Durga.
>
>
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
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From: <kad...@gm...> - 2004-04-21 15:39:46
|
Hi Harry and Jason, Here is what it today morning from the beginning : As Root: I changed my pg_hba.conf file according to Harry's file. I also changed the LOCAL_DIR , in GeneX.conf file to point to "/user/local" then : As User :kaddepal $ svn update $ make configure and then again as root: make install Errors: when I did svn update : kaddepal@1[genex-server]$ svn update svn: Failed to add file 'Perl/scripts/create-db-roles.pl': object of the same name already exists kaddepal@1[genex-server]$ I continued. after make install : Finished Congratulations! You have successfully installed the DB into Postgres. Changing permissions on Genex trees.. You will need to add the following piece to your Apache config file: Include usr/local/genex/etc/genex.conf And restart the apache server. Whew!! Time to point your browser at: http://wellerlab2.binf.gmu.edu/genex/mason/nologin/docs/docs.html and give it a whirl. NB: If you haven't done so in a previous installation, you still have to: 1) add the text from the file [cron.entries] to the appropriate crontab =========================================================================== #### ERRORS WERE ENCOUNTERED #### There were errors in your installation. Please check the file [install-errors.txt] to see more information. Thank you! Then I added the line " Include usr/local/genex/etc/genex.conf " to httpd.conf file in the Apache folder. and then restarted apache. root@1[apache]# /etc/init.d/apache restart Configuration syntax error detected. Not reloading. [Wed Apr 21 11:14:53 2004] [warn] module perl_module is already loaded, skipping fopen: No such file or directory apache: could not open document config file /usr/local/genex/etc/genex.conf root@1[apache]# Install-errors.txt : !! System Error: No such file or directory @ line: 263 (cp Mason/comps/autohandler-top.mason !! System Error: No such file or directory @ line: 263 (cp Mason/comps/autohandler-bottom.mas ~ Durga. |
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From: <hde...@gm...> - 2004-04-20 17:44:56
|
Harry, Thats right,just wanted to sound like recipe so that people who would be interested in installing GeneX will find it easy to use, this is line with lots of help web pages one finds when installing/fixing/configuring linux systems. Also the reason i wrote it this way b'coz i have gone through the INSTALL .doc and checked the 'logic' and i guess my recipe/go and do this and then this recipe/steps helps,if i am not wrong Durga was working on this,so this might help her arrange/word the INSTALL.doc in a better way. Thanks, Hrishi ----- Original Message ----- From: Harry Mangalam <hj...@ta...> Date: Tuesday, April 20, 2004 12:58 pm Subject: Re: [Genex-users] Durga : update > Thanks Hrishi, > > In looking at the doc, the only thing I can see that you've > changed is the the > paragraph at the top, the format (MS Word), and the hiliting - is > that right? > Or are there content changes later in the text as well? > > I thank you for the input - you and Durga have been quite helpful > in pinpointing > badly worded sections and bugs, but in keeping with the KISS > principle that you > stated, we're going to keep it plain text until we change it to an > HTML doc, I > think. Changing to Word, expanded the size of the doc ~6x and > made it harder to > track changes (our code versioning software likes plain text). > > Thanks! the crontab mention is a left-over from the analysis stuff > that was > cleaned out. I'll modify that to remove mention of it. > > > > hjm > > hde...@gm... wrote: > > Hi All, > > > > Here is MyInstall .doc i have put down what i think one should > be doing, Harry let me know if this is sufficient or more input is > required,basically its my recipe for installing GeneX. > > > > Thanks, > > Hrishi > > > > PS:What about crontab line at the end of the installation!!! > > > > ____________________________________________________________________ > > > > '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: kad...@gm... > > Date: Tuesday, April 20, 2004 10:06 am > > Subject: [Genex-users] Durga : update > > > > > >>Hi Harry, > >>I tried again : > >>svn update > >>make configure > >> and then as root > >>make install > >> > >>While make install i said 'NO' when it asks for running the DB > >>installer - as it is clearly mentioned there that u need not > rerun > >>if it is already there. > >>The output : > >> > >> > >> NOTE: > >> > >> If you have already run the DB installer, you need not re-run > >> it now (unfortunately I have no way of knowing this, so you > >> must tell me, sorry). > >> > >> > >>>Continue installing DB? [Y] n > >> > >>Ok... Skipping installation of DB as instructed. > >> > >> > >> > >>Changing permissions on Genex trees.. > >> > >>You will need to add the following piece to your Apache config > >>file: > >> > >> Include /home/kaddepal/genex-server/genex/etc/genex.conf > >> > >>And restart the apache server. > >> > >> > >> > >>Whew!! Time to point your browser at: > >> > >>http://wellerlab2.binf.gmu.edu/genex/mason/nologin/docs/docs.html > >> > >>and give it a whirl. > >> > >>NB: If you haven't done so in a previous installation, you > still > >>have to: > >>1) add the text from the file [cron.entries] to the appropriate > >>crontab > >> > >>=========================================================================== > >> > >> #### ERRORS WERE ENCOUNTERED #### > >> > >>There were errors in your installation. Please check the file > >>[install-errors.txt] to see more information. > >> > >>Thank you! > >> > >>Then I restarted the apache server: > >> > >>root@1[apache]# /etc/init.d/apache restart > >>Configuration syntax error detected. Not reloading. > >> > >>[Tue Apr 20 10:00:34 2004] [warn] module perl_module is already > >>loaded, skipping > >>fopen: No such file or directory > >>apache: could not open document config file > >>/usr/local/genex/etc/genex.confroot@1[apache]# > >> > >>Whats wrong??? something in pg_hba.conf ? > >>Durga. > >> > >> > >> > >>------------------------------------------------------- > >>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>> > > > ------------------------------------------------------- > 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 > > |
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From: Harry M. <hj...@ta...> - 2004-04-20 16:58:13
|
Thanks Hrishi, In looking at the doc, the only thing I can see that you've changed is the the paragraph at the top, the format (MS Word), and the hiliting - is that right? Or are there content changes later in the text as well? I thank you for the input - you and Durga have been quite helpful in pinpointing badly worded sections and bugs, but in keeping with the KISS principle that you stated, we're going to keep it plain text until we change it to an HTML doc, I think. Changing to Word, expanded the size of the doc ~6x and made it harder to track changes (our code versioning software likes plain text). Thanks! the crontab mention is a left-over from the analysis stuff that was cleaned out. I'll modify that to remove mention of it. hjm hde...@gm... wrote: > Hi All, > > Here is MyInstall .doc i have put down what i think one should be doing, Harry let me know if this is sufficient or more input is required,basically its my recipe for installing GeneX. > > Thanks, > Hrishi > > PS:What about crontab line at the end of the installation!!! > > ____________________________________________________________________ > > '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: kad...@gm... > Date: Tuesday, April 20, 2004 10:06 am > Subject: [Genex-users] Durga : update > > >>Hi Harry, >>I tried again : >>svn update >>make configure >> and then as root >>make install >> >>While make install i said 'NO' when it asks for running the DB >>installer - as it is clearly mentioned there that u need not rerun >>if it is already there. >>The output : >> >> >> NOTE: >> >> If you have already run the DB installer, you need not re-run >> it now (unfortunately I have no way of knowing this, so you >> must tell me, sorry). >> >> >>>Continue installing DB? [Y] n >> >>Ok... Skipping installation of DB as instructed. >> >> >> >>Changing permissions on Genex trees.. >> >>You will need to add the following piece to your Apache config >>file: >> >> Include /home/kaddepal/genex-server/genex/etc/genex.conf >> >>And restart the apache server. >> >> >> >>Whew!! Time to point your browser at: >> >>http://wellerlab2.binf.gmu.edu/genex/mason/nologin/docs/docs.html >> >>and give it a whirl. >> >>NB: If you haven't done so in a previous installation, you still >>have to: >>1) add the text from the file [cron.entries] to the appropriate >>crontab >> >>=========================================================================== >> >> #### ERRORS WERE ENCOUNTERED #### >> >>There were errors in your installation. Please check the file >>[install-errors.txt] to see more information. >> >>Thank you! >> >>Then I restarted the apache server: >> >>root@1[apache]# /etc/init.d/apache restart >>Configuration syntax error detected. Not reloading. >> >>[Tue Apr 20 10:00:34 2004] [warn] module perl_module is already >>loaded, skipping >>fopen: No such file or directory >>apache: could not open document config file >>/usr/local/genex/etc/genex.confroot@1[apache]# >> >>Whats wrong??? something in pg_hba.conf ? >>Durga. >> >> >> >>------------------------------------------------------- >>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>> |
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From: <ja...@op...> - 2004-04-20 15:41:25
|
hde...@gm... writes: > GeneX Works,GeneX works. The link works. Good deal. Now all we need to do is test the system, again, and again, and again ... Cheers, jas. |
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From: <ja...@op...> - 2004-04-20 15:40:36
|
kad...@gm... writes: > You will need to add the following piece to your Apache config > file: > > Include /home/kaddepal/genex-server/genex/etc/genex.conf ??? Um... This looks *highly* suspicious. LOCAL_DIR is misconfigured in GeneX.config. You have configured LOCAL_DIR to point to were the genex source code lives '/home/kaddepal/genex-server/' instead of where you want the files to get installed, e.g. '/usr/local'. Harry, I have updated the documentation for this in GeneX.config but this happened to another volunteer I was working with here in Bangalore today as well. I really think we should rename this variable to something closer to what it does - like INSTALL_PREFIX, or we will have a lot more people misconfiguring it. Shall I go ahead? Cheers, jas. |
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From: Harry M. <hj...@ta...> - 2004-04-20 14:47:52
|
That's (pedantically) true. However, it does assume that the DB installer has been run /successfully/, which has not been the case yet. I'll modify the installer script to be clearer on this point. Short version - you need to run the DB installer again. hjm kad...@gm... wrote: > Hi Harry, > I tried again : > svn update > make configure > and then as root > make install > > While make install i said 'NO' when it asks for running the DB installer - as it is clearly mentioned there that u need not rerun if it is already there. > The output : > > > NOTE: > > If you have already run the DB installer, you need not re-run > it now (unfortunately I have no way of knowing this, so you > must tell me, sorry). > > >>Continue installing DB? [Y] n > > > Ok... Skipping installation of DB as instructed. > > > > Changing permissions on Genex trees.. > > You will need to add the following piece to your Apache config > file: > > Include /home/kaddepal/genex-server/genex/etc/genex.conf > > And restart the apache server. > > > > Whew!! Time to point your browser at: > > http://wellerlab2.binf.gmu.edu/genex/mason/nologin/docs/docs.html > > and give it a whirl. > > NB: If you haven't done so in a previous installation, you still have to: > 1) add the text from the file [cron.entries] to the appropriate crontab > > > =========================================================================== > > #### ERRORS WERE ENCOUNTERED #### > > There were errors in your installation. Please check the file > [install-errors.txt] to see more information. > > Thank you! > > Then I restarted the apache server: > > root@1[apache]# /etc/init.d/apache restart > Configuration syntax error detected. Not reloading. > > [Tue Apr 20 10:00:34 2004] [warn] module perl_module is already loaded, skipping > fopen: No such file or directory > apache: could not open document config file /usr/local/genex/etc/genex.conf > root@1[apache]# > > Whats wrong??? something in pg_hba.conf ? > Durga. > > -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... <<plain text preferred>> |
|
From: <kad...@gm...> - 2004-04-20 14:26:37
|
Hi Harry,
I tried again :
svn update
make configure
and then as root
make install
While make install i said 'NO' when it asks for running the DB installer - as it is clearly mentioned there that u need not rerun if it is already there.
The output :
NOTE:
If you have already run the DB installer, you need not re-run
it now (unfortunately I have no way of knowing this, so you
must tell me, sorry).
> Continue installing DB? [Y] n
Ok... Skipping installation of DB as instructed.
Changing permissions on Genex trees..
You will need to add the following piece to your Apache config
file:
Include /home/kaddepal/genex-server/genex/etc/genex.conf
And restart the apache server.
Whew!! Time to point your browser at:
http://wellerlab2.binf.gmu.edu/genex/mason/nologin/docs/docs.html
and give it a whirl.
NB: If you haven't done so in a previous installation, you still have to:
1) add the text from the file [cron.entries] to the appropriate crontab
===========================================================================
#### ERRORS WERE ENCOUNTERED ####
There were errors in your installation. Please check the file
[install-errors.txt] to see more information.
Thank you!
Then I restarted the apache server:
root@1[apache]# /etc/init.d/apache restart
Configuration syntax error detected. Not reloading.
[Tue Apr 20 10:00:34 2004] [warn] module perl_module is already loaded, skipping
fopen: No such file or directory
apache: could not open document config file /usr/local/genex/etc/genex.conf
root@1[apache]#
Whats wrong??? something in pg_hba.conf ?
Durga.
|
|
From: <hde...@gm...> - 2004-04-20 11:09:52
|
GeneX Works,GeneX works. The link works. -Hrishi |
|
From: <hde...@gm...> - 2004-04-19 23:36:39
|
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>>
>
>
|
|
From: Harry M. <hj...@ta...> - 2004-04-19 21:25:50
|
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>>
|
|
From: <hde...@gm...> - 2004-04-19 20:46:47
|
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
|
|
From: <hde...@gm...> - 2004-04-19 20:11:05
|
Hi Harry,
Here's the error which i get when i make install, i did make Makefile=
.PL; make install by cd Perl/Class.... dirs
Apart from this there is one more problem,i did make configure as roo=
t!!!!the second time i tried after doing make install Perl/Class.....=
........ dirs
Now how does one "unroot" them all at once!!!!
Waiting for your reply.
Can't believe it that i committed this harakiri :(
Thanks,
Hrishi
Creating DB ...
/usr/local/genex/bin/create-genex-db.pl --dbname genex --user=
name genex --password --rootdir /home/deshmuk/genex-server /home/des=
hmuk/genex-server/DB/xml/GENEX_ARRAY.xml /home/deshmuk/genex-server/D=
B/xml/GENEX_ARRAY_DESIGN.xml /home/deshmuk/genex-server/DB/xml/GENEX_=
ARRAY_MANUFACTURE.xml /home/deshmuk/genex-server/DB/xml/GENEX_AUDIT.x=
ml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL.xml /home/desh=
muk/genex-server/DB/xml/GENEX_BIOMATERIAL_CHARACTERISTIC.xml /home/de=
shmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_LINK.xml /home/deshmuk/ge=
nex-server/DB/xml/GENEX_CHANGELOG.xml /home/deshmuk/genex-server/DB/x=
ml/GENEX_CHROMOSOME.xml /home/deshmuk/genex-server/DB/xml/GENEX_CITAT=
ION.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE.xm=
l /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE_LINK.xml=
/home/deshmuk/genex-server/DB/xml/GENEX_CONTACT.xml /home/deshmuk/ge=
nex-server/DB/xml/GENEX_CONTROLLED_VOCAB.xml /home/deshmuk/genex-serv=
er/DB/xml/GENEX_DATABASE.xml /ho.........................
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
____________________________________________________________________
'Life's battles don't always go to the stronger or faster man. But so=
oner or later the man who wins is the one who thinks he can.'
-Walter D. Wintle=20
----- Original Message -----
=46rom: Harry Mangalam <hj...@ta...>
Date: Monday, April 19, 2004 3:19 pm
Subject: [Genex-users] Re:
> 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
>=20
> -------------------------------------------------------
> 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=3D1470&alloc_id=3D3638&op=
=3Dclick
> _______________________________________________
> Genex-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-users
>=20
>=20
|
|
From: <hde...@gm...> - 2004-04-19 19:46:26
|
Gotcha, found the .config file in etc dir. Thx, 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 3:19 pm Subject: [Genex-users] Re: > 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>> > > > ------------------------------------------------------- > 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 > > |
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From: <hde...@gm...> - 2004-04-19 19:46:25
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Hi Harry, GeneX.config is supposed to be in genex-server dir after i do svn................................... I can't find the same in genex-server, i am done with the first part of the INSTALL only editing this .config file and then make configure;install remain. Waiting for your reply. Thanks, 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 3:19 pm Subject: [Genex-users] Re: > 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>> > > > ------------------------------------------------------- > 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 > > |
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