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From: Todd F. P. <tf...@nc...> - 2001-10-28 22:44:35
|
Matt: Ran through the tutorial on my own on our sample database and reproduced the error message. We will check into the problem and keep you informed. Todd On Sun, 28 Oct 2001, Todd F. Peterson wrote: > Matt: > > Ary you using your GeneX Server to do the tutorial or ours? > > Todd Peterson > NCGR > > On Sun, 28 Oct 2001, Matthew Lin wrote: > > > Hi Harry, > > I don't quite understand what you were saying. I didn't change any scripts. I just followed the CyberT tutorial and use the given data set file, "yeast64.cybert.demo.txt". Then I got the error message that I told you before. Please give me some suggestions of fixing the problem. Thank you > > > > P.S. I have attaced the yeast64.cybert.demo.txt with this email in case you need it. > > > > > > Matt > > 3:40pm > > 10/28/2001 > > > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev > |
|
From: Matthew L. <ma...@jh...> - 2001-10-28 22:31:27
|
Todd,
I tried both, and I got the same error message.
Matt
5:29pm
10/28/2001
|
|
From: Todd F. P. <tf...@nc...> - 2001-10-28 22:29:00
|
Matt: Ary you using your GeneX Server to do the tutorial or ours? Todd Peterson NCGR On Sun, 28 Oct 2001, Matthew Lin wrote: > Hi Harry, > I don't quite understand what you were saying. I didn't change any scripts. I just followed the CyberT tutorial and use the given data set file, "yeast64.cybert.demo.txt". Then I got the error message that I told you before. Please give me some suggestions of fixing the problem. Thank you > > P.S. I have attaced the yeast64.cybert.demo.txt with this email in case you need it. > > > Matt > 3:40pm > 10/28/2001 > |
|
From: Matthew L. <ma...@jh...> - 2001-10-28 20:43:11
|
YLL005C 0.74972067 1.036898396 1.27625 2.960725076 7.959237692 = 4.962075848 4.285714286=0A= YLL006w 0.756981383 0.900197628 0.866666667 0.916666667 1.362385321 = 0.980828221 0.935205184=0A= YLL007C 0.735215054 1.03151422 0.776212833 0.728278041 0.670789724 = 0.649550706 0.728813559=0A= YLL008w 0.73757349 0.19331555 0.325745683 0.572086596 1.346621979 = 1.548855794 1.395209581=0A= YLL009c 0.722436722 0.453783584 0.409953822 0.443426724 0.35040729 = 0.448717949 0.50147929=0A= YLL010C 0.864840989 0.707455013 0.832037325 0.849254555 0.71637744 = 0.889992057 0.859649123=0A= YLR437C 1.190633811 0.88115747 0.823960586 0.920962199 0.890453653 = 0.87734386 0.906006887=0A= YLR438W 0.971342383 7.602150538 6.041793313 5.844604317 5.858468677 = 3.373033708 3.643652561=0A= YNR021W 0.840405558 0.476110925 0.792741165 0.474133333 0.336707292 = 0.394243349 0.404208195=0A= YNR022C 0.62485833 0.367739994 0.524093124 0.596868885 0.592720427 = 0.544508671 0.511131725=0A= YNR023W 0.898945518 0.824571112 0.986085904 1.144947735 1.479116141 = 1.451051051 1.12611276=0A= YNR024W 0.71460177 0.423438549 0.915782024 1.672906404 1.815691869 = 1.430182808 1.293726937=0A= YNR025C 0.752318393 0.425 0.938380282 1.549647662 2.237699238 = 1.849795441 1.503546099=0A= YNR026C 1.411764706 0.584327087 0.703517588 1.439613527 4.263829787 = 2.796992481 3.606060606=0A= YNR027W 0.804131599 0.706666667 0.910813824 0.991399531 0.791006966 = 0.925 0.748148148=0A= YNR028W 0.702739726 0.9862107 1.257925072 1.0625 1.050859107 1.003984064 = 0.895256917=0A= YOL151W 1.069058296 0.294772922 0.645933014 0.214227971 0.52352623 = 0.345767575 0.634146341=0A= YOL152W 0.747336377 0.269823789 0.678004535 0.476878613 0.518950437 = 0.637181409 0.667741935=0A= YOL153C 0.862035032 1.433375905 1.095409541 0.632102787 0.411326103 = 0.395302897 0.469141997=0A= YOL154W 0.712835985 1.435602711 1.501775748 1.452615225 2.304055353 = 1.61802693 1.475375842=0A= YOL155C 0.988804446 0.752901692 0.611910338 0.56678255 0.648333959 = 0.499382157 0.743233176=0A= YOL156W 0.791759964 1.279104038 1.32398957 2.256265158 2.725679229 = 2.471011236 2.124382208=0A= YOL157C 0.942122186 1.204966772 0.624453087 0.657328222 1.315552699 = 1.363673386 1.506756757=0A= YOL158C 0.765725654 0.216395565 0.274417351 0.120692471 0.113978839 = 0.123028896 0.110162794=0A= YOL159C 0.685950413 0.526315789 0.587973274 0.680473373 0.832201087 = 0.853658537 0.605150215=0A= YOL160W 0.736714976 0.657568238 0.578723404 0.534090909 0.548648649 = 0.776435045 0.505928854=0A= YOL161C 0.833396874 0.983341747 1.306196841 1.125679348 1.714243845 = 1.633851468 1.555921053=0A= YOL162W 0.662824207 0.508982036 0.68907563 0.494071146 0.662576687 = 0.879166667 0.670807453=0A= YOL163W 1.103773585 0.45323741 0.622807018 0.951428571 0.866432337 = 1.197718631 0.929824561=0A= YOR298W 0.525350593 0.316445183 1.065810594 3.149753695 10.07227891 = 7.816252588 4.526276276=0A= YOR299W 0.82770928 0.27053402 0.209404389 0.125878399 0.083869628 = 0.131311192 0.116689281=0A= YOR300W 0.660381697 0.476609105 0.307719422 0.330367075 0.234893125 = 0.280797741 0.327561737=0A= YOR301W 0.864442127 0.896733404 1.290381125 1.264705882 3.107988166 = 3.114888628 1.94092827=0A= YOR302W 0.739212598 1.177105832 0.559537572 0.701308699 0.515146084 = 0.579567308 0.586749482=0A= YPR026W 0.787181594 1.351118761 0.970190779 1.02406639 0.967867868 = 1.040905481 1.150364964=0A= YPR027C 0.810756972 0.793205318 0.918287938 4.635157546 8.003 = 6.306930693 7.148337596=0A= YPR028W 0.810800158 0.648533951 1.166998012 0.605511811 0.569255839 = 1.078214286 1.10588843=0A= YPR029C 0.729217307 1.57654321 1.538123167 2.039162113 2.239243499 = 1.965877821 1.644194757=0A= YPR030W 0.750070363 0.297314578 0.284550898 0.390747331 0.24084524 = 0.222785421 0.274127775=0A= YPR031W 0.589130435 1.201322557 1.411706349 1.75308642 2.037435897 = 2.370275464 2.199228792=0A= YPR032W 0.777555911 0.75712881 1.003508772 1.620618557 1.102158711 = 0.714675396 0.749659864=0A= YPR033C 0.688584848 0.45521914 0.740410959 0.638588503 0.42208384 = 0.449960907 0.428632662=0A= YPR034W 0.729296066 0.952631579 0.89438577 0.951721055 0.860164934 = 0.77281309 0.798830409=0A= YPR135W 0.818904594 0.785608309 0.70042796 0.671215881 0.85520362 = 0.789581205 0.78375286=0A= YPR136C 0.80620915 0.207053073 0.321487603 0.391621129 0.236134657 = 0.321977288 0.558998808=0A= YPR137W 0.688995215 0.625 0.982954545 0.543568465 0.665957447 = 1.056737589 0.827586207=0A= YPR188C 1.095419847 0.881613757 1.288764045 0.945175439 0.792710706 = 0.614783227 0.679935012=0A= YPR189W 1.106936416 0.605718585 0.76673428 0.717850288 0.858156028 = 0.839572193 0.793103448=0A= YPR190C 0.921760391 0.243992606 0.525704809 0.714691558 0.854695431 = 0.939557961 0.864171864=0A= YPR191W 0.891241578 0.599527466 0.847688123 0.767676768 0.630051224 = 0.612435233 0.568055556=0A= YPR192W 0.770121279 0.672701201 3.613464448 3.801123596 2.222076216 = 2.892908828 1.975957257=0A= YPR193C 0.817922607 0.776884071 2.302966102 2.297169811 1.706956248 = 1.587728741 1.186979561=0A= YPR194C 0.790806129 1.144200627 1.476311337 1.509360878 2.027737226 = 2.359557468 2.484187568=0A= YPR195C 0.848996832 0.680738786 0.735733099 0.803585982 0.811141304 = 0.899707887 0.948121646=0A= YPR196W 0.661347518 0.794219653 0.765550239 0.718562874 1.068820225 = 0.848484848 0.569587629=0A= YPR197C 0.750827423 1.175462336 1.327469553 1.166137566 1.219127693 = 0.994634474 1.118570183=0A= YPR198W 1.027027027 0.908108108 0.919117647 0.907090465 0.73553719 = 1.051085568 0.653061224=0A= YPR199C 0.828042328 0.602905569 0.648255814 0.709821429 0.683950617 = 0.859477124 0.734439834=0A= YPR200C 0.788511749 0.767088608 0.703412073 0.873563218 0.725868726 = 0.972058824 0.72244898=0A= YPR201W 0.743055556 0.462633452 0.605015674 0.524904215 0.838383838 = 1.07751938 0.744292237=0A= YPR202W 0.746581077 0.961462058 1.836495889 1.427680798 1.066948555 = 0.84623431 0.863374486=0A= YPR203W 0.658364187 1.0512876 1.239949109 1.231168831 0.995283019 = 0.763039656 0.756166983=0A= YPR204W 0.749275922 1.398144057 1.523262493 1.113456069 1.134607464 = 0.774500673 0.832629108=0A= YBR214W 1.270686567 1.364384367 0.831270627 0.445238422 0.374943328 = 0.28820598 0.481899048=0A= |
|
From: Harry M. <man...@ho...> - 2001-10-28 20:07:28
|
Hmm - you've managed to reach a point in the script that should have been unreachable - that error message could only have been reached if neither hard-coded alternative values were true.
When you ask for help, it's a good thing to tell what dataset you were using (and generate the minimum dataset nec. to replicate the problem and include it (or a pointer to it would be better) and the
parameters you used to generate the error.
Also, did this error occur when you submitted the error to the genex site (or was the data extracted from your database?)
Right now all I can tell you is the above, which seems to indicate that something changed the script code, since this error message should never have been reached (altho god knows there are enough
weird conditions that I've probably never considered that it might have gotten there)...
Lemme know the above parameters and I can help you more.
hjm
> Matthew Lin wrote:
>
> When I tried to run CyberT, I got the following error message from the browser:
>
>
> Content-type: text/html
>
> Software error:
>
> <b>The Low value params have been messed up in some way - please check them</b> at /var/www/cgi-bin/genex/cybert/CyberTDB-7.0.pl line 192
>
> Please give me some pointers. Thank you
>
> Matt
> 2:39pm
> 10/28/2001
--
Cheers, Harry
Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
[plain text appreciated]
|
|
From: Matthew L. <ma...@jh...> - 2001-10-28 19:41:59
|
When I tried to run CyberT, I got the following error message = from the browser: Content-type: text/html=20 Software error: <b>The Low value params have been messed up in some way - please check = them</b> at /var/www/cgi-bin/genex/cybert/CyberTDB-7.0.pl line 192 Please give me some pointers. Thank you Matt2:39pm10/28/2001 |
|
From: Todd F. P. <tf...@nc...> - 2001-10-27 19:29:24
|
Matthew Looked at the file and seems ok. As Jason said, the Perl libraries might not be able to be found. Try running the perl script directly from the command line on your GeneX Server (like this): temp 64 % !g generate-expset.pl Can't locate LoginUtil.pm in @INC (@INC contains: /usr/local/genex/perl5 /usr/lo cal/lib/perl5/sun4-solaris/5.00404 /usr/local/lib/perl5 /usr/local/lib/perl5/sit e_perl/sun4-solaris /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/sun4-sol aris) at generate-expset.pl line 40. BEGIN failed--compilation aborted at generate-expset.pl line 40. What this is saying is that a required Perl module, LoginUtil.pm, couldn't be found (in the system I ran this on...which is not set up for GeneX). Another problem could be the first line: #! /usr/bin/perl -wF The script assumes your perl is at /usr/bin/perl. In my case it was at /usr/local/bin/perl so I had to change the first line to match the system I ran on. alternatively, i could have just typed 'perl generate-expset.pl'. To determine where your Perl executable is type 'which perl' or 'locate perl' Hope this helps. Todd Peterson NCGR On Fri, 26 Oct 2001, Matthew Lin wrote: > > |
|
From: Harry M. <man...@ho...> - 2001-10-26 21:46:42
|
Hi Greg,
Sorry for the delay.
Michael, please jump in to correct mistakes.
As I read it, the 'provider' commandline key is the contact key in your database. In michael's code, this is hardcoded as a default relevant to his database (544) so it's not surprising that it
failed for you.
You have to either give it the appro numeric key for your installation &| change the hardcoded value to be the correct value for your DB.
loadaffylayout.pl [29]:
$contact_key = exists($OPTIONS{provider})?$OPTIONS{provider}:544;
You'll have to query your DB installation to figure out what this value is:
psql genex
genex=# select con_pk from contact;
con_pk
--------
6
85
86
80
7
81
82
83
84
etc whic indicates ALL con_PKs - you probably want to use the one for teh curator which would be:
select * from contact where Type='curator';
or you may be able to set a new one by just giving it on the commandline.
The table looks like this and what it's looking for is the con_pk
(where '+' indicates a wrapped line)
genex-# \d contact
Table "contact"
Attribute | Type | Modifier
----------------------+--------------+----------------------------------- +
-------------------
con_pk | integer | not null default + nextval('contact_con_pk_seq'::text)
type | varchar(128) | not null
organization | varchar(128) | not null
contact_person | varchar(128) |
contact_person_phone | varchar(128) |
contact_person_email | varchar(128) |
org_phone | varchar(128) |
org_email | varchar(128) |
org_mail_address | varchar(128) |
org_toll_free_phone | varchar(128) |
org_fax | varchar(128) |
url | varchar(128) |
last_updated | timestamp | not null
Index: contact_pkey
In browsing around this file, there appear to be some more MPear-specific hard-codes that you'll probably have to change as well.
> Greg Riddick wrote:
>
> Hi,
>
> I'm a graduate student working on getting GENEX installed here. We're working with a (beta?) version of the Affymetrix uploader.
> We're a little confused about what the provider command-line option is for. The default value (544) doesn't seem to be working for us.
> Any help would be appreciated.
>
> Thanks,
> Greg Riddick
--
Cheers, Harry
Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
[plain text appreciated]
|
|
From: <ja...@op...> - 2001-10-26 18:46:10
|
"Matthew Lin" <ma...@jh...> writes: > Then I checked the apache server on the GeneX server, I found the following message in the server log file: > > > [Mon Oct 26 11:36:36 2020] [error] [client 128.220.136.34] Premature end of script headers: /var/www/cgi/bin/genex/curation-tool/generate-expset.pl This is the standard message that appears after the script has died. What is informative, is what appears *before* this entry. It will say things like "Couldn't locate file Foo.pm in @INC" or some database access "Permission Denied" problem. jas. |
|
From: Harry M. <man...@ho...> - 2001-10-26 17:38:20
|
Hi Greg,
I'm just about to start a teleconf so I'll help you out after it ends, OK?
The very short version is that Michael Pear wrote it so if I can't determine what the problem is, I'll have to go to him (if he's not getting this directly from the list). He now has a day job and
therefore real responsibilities ;) so he may not be able to answer until this evening.
hjm
> Greg Riddick wrote:
>
> Hi,
>
> I'm a graduate student working on getting GENEX installed here. We're working with a (beta?) version of the Affymetrix uploader.
> We're a little confused about what the provider command-line option is for. The default value (544) doesn't seem to be working for us.
> Any help would be appreciated.
>
> Thanks,
> Greg Riddick
--
Cheers, Harry
Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
[plain text appreciated]
|
|
From: Greg R. <gr...@vi...> - 2001-10-26 17:20:44
|
Hi, I'm a graduate student working on getting GENEX installed here. We're = working with a (beta?) version of the Affymetrix uploader. We're a little confused about what the provider command-line option is = for. The default value (544) doesn't seem to be working for us. Any help would be appreciated. Thanks, Greg Riddick |
|
From: Todd F. P. <tf...@nc...> - 2001-10-26 16:25:53
|
Please send the generate-expset.pl file...maybe it will provide us with some clues. Todd On Fri, 26 Oct 2001, Matthew Lin wrote: > Hi, > I was trying to download an exp set from a client computer. After I logged into GeneX server and tried to dowload data, I got this message from my brower: > > Internal Server Error > The server encountered an internal error or misconfiguration and was unable to complete your request. > Please contact the server administrator, root@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error. > > More information about this error may be available in the server error log. > > > > Then I checked the apache server on the GeneX server, I found the following message in the server log file: > > > [Mon Oct 26 11:36:36 2020] [error] [client 128.220.136.34] Premature end of script headers: /var/www/cgi/bin/genex/curation-tool/generate-expset.pl > > > > I assume there is something wrong with "generate-expset.pl", but I don't know which line in the file causes this error. Please give me some pointers. Thank you > > > > Matt > 12:15pm > 10/26/2001 > > > > > > > > > > > > > > > > |
|
From: Matthew L. <ma...@jh...> - 2001-10-26 16:18:54
|
Hi,
I was trying to download an exp set from a client computer. =
After I logged into GeneX server and tried to dowload data, I got this =
message from my brower:
Internal Server Error
The server encountered an internal error or misconfiguration and was =
unable to complete your request.=20
Please contact the server administrator, root@localhost and inform them =
of the time the error occurred, and anything you might have done that =
may have caused the error.=20
More information about this error may be available in the server error =
log.
Then I checked the apache server on the GeneX server, I found the =
following message in the server log file:
[Mon Oct 26 11:36:36 2020] [error] [client 128.220.136.34] Premature end =
of script headers: =
/var/www/cgi/bin/genex/curation-tool/generate-expset.pl
I assume there is something wrong with "generate-expset.pl", but I don't =
know which line in the file causes this error. Please give me some =
pointers. Thank you
Matt
12:15pm
10/26/2001
|
|
From: <ja...@op...> - 2001-10-26 15:43:08
|
Hey, If you have configured your genex server's postgres installation to accept internet socket connections, you *could* run it on the client computer, but I wouldn't do that, because it makes your system far too vulnerable to someone snooping around. I would run everything on the server, and restrict access to the server machine. And you can run it as any user. The only time you should need to be root or postgres is during installation. This is because the GeneX module records the password info for the database account 'genex' in the module. So anyone with login permission to the server can access and modify any data in the DB. jas. "Todd F. Peterson" <tf...@nc...> writes: > You need to run xml2db.pl on the server but you do not have to be > root. Note that the program first looks in the cache directory > before generating output. That is, if the control bundle or > experiment set files exist in the cache, the program exits. So, you > must delete the files in the cache first. > > Todd Peterson > NCGR > > On Fri, 26 Oct 2001, Matthew Lin wrote: > > > Hi, > > I have couple questions about xml2db.pl. I wonder if it is > > possible to run xml2db.pl on a client computer or I have > > to run this command on GeneX server. If I had to run it on > > the GeneX server, can I run it as "root" or I have to > > login as postgres and run the command? Thank you |
|
From: Todd F. P. <tf...@nc...> - 2001-10-26 15:00:12
|
Matt: You need to run xml2db.pl on the server but you do not have to be root. Note that the program first looks in the cache directory before generating output. That is, if the control bundle or experiment set files exist in the cache, the program exits. So, you must delete the files in the cache first. Todd Peterson NCGR On Fri, 26 Oct 2001, Matthew Lin wrote: > Hi, > I have couple questions about xml2db.pl. I wonder if it is possible to run xml2db.pl on a client computer or I have to run this command on GeneX server. If I had to run it on the GeneX server, can I run it as "root" or I have to login as postgres and run the command? Thank you > > > Matt > 10:37pm > 10/26/2001 > |
|
From: Matthew L. <ma...@jh...> - 2001-10-26 14:39:49
|
Hi,
I have couple questions about xml2db.pl. I wonder if it is =
possible to run xml2db.pl on a client computer or I have to run this =
command on GeneX server. If I had to run it on the GeneX server, can I =
run it as "root" or I have to login as postgres and run the command? =
Thank you
Matt
10:37pm
10/26/2001
|
|
From: Harry M. <man...@ho...> - 2001-10-25 15:47:01
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Hi Cheol, Like Todd has indicated, There are 2 main parts of the GeneX system - the web database & analysis server (which runs on unix/Linux) and the Curation Tool to lad teh data into the database which is written in Java and should therefore run on multiple platforms, including win32 systems. GeneX is mostly a database system, so if you just want to cluster a large dataset, it will not be that useful to you - try Bjarte Dysvik's J-Express: http://www.molmine.com or Stanford's xcluster: http://genome-www.stanford.edu/~sherlock/cluster.html if you want a free, high quality clustering application. J-Express is Java and will run on win32 xcluster is an improved unix port of the original cluster program which is win32-native. Both will generate the popular Eisen diagrams. J-Express is the better of the 2 in terms of interfacee design and what techniques you can apply to the data, however since it is a Java program, it is almost by definition a memory catastrophe when dealing with large amounts of data, and you will have to manually pre-allocate RAM to it for large datasets. If you want to try teh analysis features of GeneX, you can upload your data in a simple tab-delimited format to the GeneX site at NCGR to analyse it directly as well. There is a significance testing application and 2 clustering applications (including stanford's xcluster), so you can see if it's worth installing. Cheers Harry "che...@sn..." wrote: > > Dear GeneX developer/personnel/lover > > Thanks Todd ... two questions to begin with (already...).... > > I was able to download the program but am not able to install the program... OS is Windows 2000 and I got GeneX for Windows 95, 98... I thought this would not be the problem... > > I have a huge set of bovine gene that sequencing has been done and am trying to grouping/clustering them regard to their function using hopefully GeneX... Can I do that? > > Thanks a million ^ million in advance > > Cheol > > Cheol H. Yun, Ph. D. > IVI, WHO > > Cheol H. Yun, Ph. D., Research professor > Department of Animal Science & Technology > College of Agriculture and Life Sciences > Seoul National University > Suwon 441-744 > S-Korea > > Phone (lab): 011-82-31-290-2648 > Phone (home): 011-82-31-291-4596 > Handphone: 011-9096-2073 > Fax: 011-82-31-294-1340 > E-mail: Che...@sn...; che...@ya... -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... [plain text appreciated] |
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From: Todd F. P. <tf...@nc...> - 2001-10-25 05:20:44
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Dear Cheol: The GeneX server has been successfully installed on Linux and Solaris (Sun). I am currently attempting to coerce the system to install on Windows 2000 and am stuck at a point where some Perl modules will not install due to some other required program (expat). The Expat is supposed to provide XML parsing that is required by the Perl module in question (XML:something). The recommended approach is to find a Linux or Solaris machine to use as the GeneX Server. The installation is tricky and requires full administrative privileges on the install machine. Please be sure to read the installation instructions carefully. The steps must be performed in a specific order (and with success). Once the GeneX Server is working properly, the Curation Tool may be used to browse and upload data. The Curation Tool may be downloaded and evaluated using a public GeneX Server at NCGR. The tutorials on the Curation Tool explain the process. The username/password to access this public GeneX Server is test/test. This avoids you having to install the GeneX Server at your location and lets you check out the user interface for curation. Web demos are also available that allow you to browse and analyze the data on this server (genex.ncgr.org). I hope this helps you out. Don't hesitate to ask more questions or provide feedback to us. Sincerely, Todd Peterson Software Developer NCGR On Thu, 25 Oct 2001, che...@sn... wrote: > Dear GeneX developer/personnel/lover > > Thanks Todd ... two questions to begin with (already...).... > > I was able to download the program but am not able to install the program... OS is Windows 2000 and I got GeneX for Windows 95, 98... I thought this would not be the problem... > > I have a huge set of bovine gene that sequencing has been done and am trying to grouping/clustering them regard to their function using hopefully GeneX... Can I do that? > > Thanks a million ^ million in advance > > Cheol > > > > Cheol H. Yun, Ph. D. > IVI, WHO > > Cheol H. Yun, Ph. D., Research professor Department of Animal Science & Technology College of Agriculture and Life Sciences Seoul National University Suwon 441-744 S-Korea Phone (lab): 011-82-31-290-2648 Phone (home): 011-82-31-291-4596 Handphone: 011-9096-2073 Fax: 011-82-31-294-1340 E-mail: Che...@sn...; che...@ya... |
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From: <che...@sn...> - 2001-10-25 03:36:07
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From: <ja...@op...> - 2001-10-24 20:31:27
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"Matthew Lin" <ma...@jh...> writes: > What is Control-Bundle file? and wat does it do? Can I add more file > into it? The control bundle is quite a messy issue. It stems from the original design of the curation tool as an application used by researchers to upload data to a central repository (i.e. NCGR). Over time the goals changed. Now the vision is that researchers will load data into their own GeneX installations in order to analyze them, etc. Because of it's original design decisions, the current curation tool has no ability to communicate with a GeneX DB, instead it must receive information via GeneXML files. So ... The control bundle is a GeneXML file exported from a GeneX DB installation that provides certain control information to the curation tool (species and organisms, protocols, array layouts, contacts, controlled vocabularies, etc). This information is then used to populate the pull-down menus of the curation tool. It is automatically generated (using the db2xml.pl script) and it reflects the current status of your GeneX DB. As you add more information to the DB, the information in the control bundle will change. You shouldn't ever manipulate a control bundle by hand. Instead, add more data to your GeneX DB or modify db2xml.pl jas. |
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From: Matthew L. <ma...@jh...> - 2001-10-24 19:27:03
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What is Control-Bundle file? and wat does it do? Can I add more = file into it? Thank you Matt 3:24pm 10/24/2001 |
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From: <ja...@op...> - 2001-10-23 22:04:27
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"Todd F. Peterson" <tf...@nc...> writes: > Dear Matthew: > > The server installation can be pretty tricky. The Server Installation page > at http://genex.ncgr.org/INSTALL has pretty detailed information. The http > and cgi-bin directories are usually installed at /home/httpd. Actually, that's the installation root for the apache WWW server, not for cgi-bin, and it's only if you're on a RedHat based system. On debian systems it's in /var/www, if you're on some random unix machine (Irix, Solaris) then it could be in /usr/local/apache. On redhat systems cgi-bin can be in /home/httpd/cgi-bin, on debian it's often at /usr/lib/cgi-bin, and on random boxes it might be in /usr/local/apache/cgi-bin > * apache web server, configured to support Server-Side-Includes This isn't likely an SSI problem that's usually only for viewing pages out of the DocumentRoot that end in .shtml > > After I changed those URL's, I got the page can't be displaied > > message in browser. 128.220.136.28 is the IP address of the GeneX > > server. I also tried the host name, genex.wbmei.jhu.edu, instead > > of the IP address, but I got the same message in the browser. I > > have another question. Where is "cgi-bin" directory suppose to be? > > Please give me some pointers. Thank you. One of the questions that the server asks you is where your cgi-bin directory is, and then it installs the GeneX CGI scripts in that location. If you don't know where the cgi-bin directory is then you are in trouble, because that meanst that you might have installed half of the GeneX-Server someplace where it didn't want to go. If you're on linux, try: locate cgi-bin and see what you get (run 'locate cgi-bin|less' if you get too much output). jas. |
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From: <ja...@op...> - 2001-10-23 21:51:55
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"Matthew Lin" <ma...@jh...> writes: > When I tried to go to NCGR site to download control bundle files, it > asked me for login name and password. I wonder if you can give me > one. Thank you. Hey Matthew, You shouldn't need to go to the NCGR site for a control bundle download, your own local installation can create them for you. jas. |
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From: Todd F. P. <tf...@nc...> - 2001-10-23 18:15:09
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Dear Matthew: The server installation can be pretty tricky. The Server Installation page at http://genex.ncgr.org/INSTALL has pretty detailed information. The http and cgi-bin directories are usually installed at /home/httpd. There are several things that could be wrong. The most probable is that the Apache server isn't running or isn't configured properly. Here is an excerpt from the Server INstallation page: * apache web server, configured to support Server-Side-Includes (see the apache documentation about this: <URL http://httpd.apache.org/docs/mod/mod_include.html>, esp. the tutorial: <URL http://httpd.apache.org/docs/howto/ssi.html> this can often be done by adding the following lines to your [httpd.conf] or [srm.conf] file and then rebooting. AddType text/html .shtml AddHandler server-parsed .shtml I hope this helps you. Todd Peterson NCGR On Tue, 23 Oct 2001, Matthew Lin wrote: > Todd, > Sorry, I pasted the wrong URL's on the last email. The following is what I have done: > > Control Bundle URL: http://128.220.136.28/cgi-bin/genex/curation-tool/cb-login.pl > Experiment Set Submit URL: http://128.220.136.28/cgi-bin/genex/curation-tool/expset-submit.pl > Experiment Set Download URL: http://128.220.136.28/cgi-bin/genex/curation-tool/expset-login.pl > > After I changed those URL's, I got the page can't be displaied message in browser. 128.220.136.28 is the IP address of the GeneX server. I also tried the host name, genex.wbmei.jhu.edu, instead of the IP address, but I got the same message in the browser. I have another question. Where is "cgi-bin" directory suppose to be? Please give me some pointers. Thank you. > > > Matt > 1:57pm > 10/23/2001 > |
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From: Matthew L. <ma...@jh...> - 2001-10-23 18:08:07
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When I tried to go to NCGR site to download control bundle files, it = asked me for login name and password. I wonder if you can give me one. = Thank you. Matt 2:05pm 10/23/2001 |
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