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From: Shih-hsiu L. <ma...@jh...> - 2001-08-22 17:36:24
|
I followed the Curation Tool Tutorial to create a E. coli experimental data set. Do I need to run xml2db.pl by myself or the system uploads the data to postgres already? Shih-Hsiu Lin 1:34pm 8/22/2001 |
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From: Todd F. P. <tf...@nc...> - 2001-08-21 16:47:53
|
The Curation Tool is designed to work on Windows, Solaris and Linux. To get it to work with your server use File->Properties menu and change Control Bundle URL and Experiment Set Submit URL to replace genebox.ncgr.org with your-server-name. Your server should work just like http://genex.ncgr.org (which is the same as genebox.ncgr.org). To be sure the server is running type ps -ef on the command line of your server. You will get back a good sized list of processes. Somewhere in the list should be the postgres postmaster process, which will look somewhat like: postgres 790 789 0 Apr11 ? 00:00:02 /usr/bin/postmaster -i There should also be several httpd processes, which will look somewhat like: root 627 1 0 Apr11 ? 00:02:10 httpd nobody 12539 627 0 Aug17 ? 00:00:00 httpd nobody 12541 627 0 Aug17 ? 00:00:00 httpd nobody 12542 627 0 Aug17 ? 00:00:00 httpd nobody 12543 627 0 Aug17 ? 00:00:00 httpd nobody 12544 627 0 Aug17 ? 00:00:00 httpd nobody 24616 627 0 Aug20 ? 00:00:00 httpd nobody 24617 627 0 Aug20 ? 00:00:00 httpd nobody 24618 627 0 Aug20 ? 00:00:00 httpd nobody 26264 627 0 08:25 ? 00:00:00 httpd nobody 26293 627 0 09:21 ? 00:00:00 httpd by typing httpd status you should get some more info. If everything is running, then you should be able to use a web browser to navigate your server similar to ours. You might have to add the suffix /genex to your base server URL: http://your-server.jhu.edu/genex. The query tool should operate on your database then. Let me know if you have any more questions. Todd On Tue, 21 Aug 2001, Shih-hsiu Lin wrote: > Todd, > I have couple questions. Now I have GeneX server running, and I > wonder if it is possible to install Curation Tool on other computers > (Windows and Liunx), so users don't have to manage the data on the server. > Also, what do I need to install on client computers? Another question is > that I have problem retrieve data from the database. I went to > http://genex.ncgr.org and click on the Live Database at NCGR, then click > on Analysis/Query, then click Database Query. Then there is Query form, > but how can I access the data in my GeneX database? Thank you > > > Shih-Hsiu > 11:45am > 8/21/2001 > > > |
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From: <ja...@op...> - 2001-08-20 16:10:46
|
"Christina Yung" <cy...@bm...> writes:
> We've recently installed GeneX and are currently trying out its different
> functions. Since our main database software is IBM DB2 V7, we're wondering
> if we could replace PostgreSQL with DB2. If so, could you give us some
> pointers on how to do so? Specifically, how does GeneX talk to PostgreSQL
> (via ODBC?)?
Hi Christina,
That would be fascinating! Currently Postgres is the only supported
DBMS, but I've set it up so that it should be possible for any SQL92
compliant DB to be plugged in. All of this is in Perl using the Perl
DBI.
Here are the pieces that you would need to change:
* Bio::Genex::DBUtils::create_insert_sql()
* Bio::Genex::DBUtils::create_update_sql()
* Bio::Genex::DBUtils::create_select_sql()
Each of these has a piece of code similar to following:
if ($dbh->dbms() eq 'Pg') {
my @set;
my %set = %{$args{SET}};
foreach my $col (keys %set) {
push(@set, "$col=" . $dbh->quote($set{$col}));
}
my $set_string = join(',', @set);
my $sql = "UPDATE $curr_table SET $set_string";
$sql .= " WHERE $args{WHERE}" if exists $args{WHERE};
} else {
carp "Bio::Genex::DBUtils::create_update_sql: Driver ", $dbh->dbms(), " not implemented";
}
For these functions, All that you would need to do is add the name of
the DBD driver for DB2 (probably just 'DB2') as a clause in the if
statement. If DB2 is SQL92 compliant, you should just be able to add:
if ($dbh->dbms() eq 'Pg' || $dbh->dbms() eq 'DB2') {
Problem #1
==========
In the current stable release of Genex, 1.0.4, we use hard-coded
Postgres SQL scripts to create the DB. In the developers version, we
have added a DBMS independent representation of the DB schema which we
parse and create DBMS-specific SQL.
If DB2 is SQL92 compliant, you should be able to directly use the
Postgres table definition scripts (located in the DB/tdscripts/
directory of the GeneX-Server packate) to create a GeneX instance in
DB2.
If you have trouble let us know, and we may be able to help.
jas.
|
|
From: Christina Y. <cy...@bm...> - 2001-08-20 15:05:36
|
We've recently installed GeneX and are currently trying out its different functions. Since our main database software is IBM DB2 V7, we're wondering if we could replace PostgreSQL with DB2. If so, could you give us some pointers on how to do so? Specifically, how does GeneX talk to PostgreSQL (via ODBC?)? Thanks, Christina ========================================== Department of Biomedical Engineering and Center for Computational Medicine & Biology The Johns Hopkins University School of Medicine Rm. 202 Clark Hall 3400 N. Charles St. Baltimore MD 21209 Phone: 410-516-5466, Fax: 410-516-5294 |
|
From: Todd F. P. <tf...@nc...> - 2001-08-19 19:16:45
|
Went through the exercise again, the coldefs are tricky. I did manage to mark up the 4 columns of data which were defined as measurement data in your original measurement column file. The key is having the column from the sequence feature file (which is also the array layout file) identified the same as the column in the spot measurement file. In your case, I identified col 2 from the layout/seq feat file to be this column since it seemed to be the only one that matched up with the values in col 1 of the measurement file. All 3 column def files must use the same notation (type and extra type) for the 'id' column. So, I used usf_name/gene_name for column 2 of the seq feature column def file. I used als_usf_name/gene_name for column 2 of the array layout column def file and I used spot_value_usf_name/gene_name for column 1 of the spot measurement column def file. The 3 files then do pass validation. Then an experiment can be created, an array layout with no errors can be created, and array measurements can be annotated. There will be errors when you save an array measurement due to there being only 4943 array layout values when there are 5184 measurements. Will try to write up some more detail on the column definition file functions. This stuff is very confusing and is one of the areas I personally plan on simplifying. Anyway, let me know if this helps at all. I will send you the write-up on the column defs ASAP. Unfortunately, it may take a while since the developer who designed this part has had severe health problems and has not been around for a while. Thank you very much for your patience and hopefully we will have your difficulties resolved soon. Todd |
|
From: <ja...@op...> - 2001-08-18 01:00:35
|
"Todd F. Peterson" <tf...@nc...> writes: > The source code is included in the developer versions of the Curation > Tool. The developer versions begin with ct150_dev. The developer versions > are available for Unix and Windows although the source code it the same. > See > http://genex.ncgr.org/genex/download/curation_tool > > The server souce code is included inside of the archive in the form of > various Perl files and Unix scripts. > > Todd > > On Fri, 17 Aug 2001, Shih-hsiu Lin wrote: > > > Where can I down load GeneX source code? If you downloaded and installed the GeneX-Server, you have all the server source code. It is a set of Perl modules, CGI scripts, and R libraries that do everything. If you are looking for CVS access to the code see: http://genex.ncgr.org/CVS.note for instructions. jas. |
|
From: <ja...@op...> - 2001-08-18 00:57:45
|
> On Fri, 17 Aug 2001, Shih-hsiu Lin wrote: > > > How does GeneX communicate with other applications such as R? I > > mean like can I open R from GeneX to perform stat. analysis on > > experiment data? Also, how can I use XCluster to work with GeneX? Hi Shih-hsiu, The GeneX-Server assumes that you are running in a Unix environment, and uses perl's system() function as well as it's qx[] (backtick) operator to run the commands directly through a shell escape. As far as getting XCluster to work, I thought there was a tutuorial available on the WWW site. jas. |
|
From: Todd F. P. <tf...@nc...> - 2001-08-17 16:50:25
|
Steffi: I am glad that you got things working! Will look into the "Browse Database" problem. Please provide the sequence of 'clicks' that triggered this problem. Specifically, the Web page address and arguments before the problem occurs and after the problem occurs. I looked in HTMLUtils.pm and it gives this message when the object it receives is not CGI. I'm not a big Perl type but should be able to track down why this happens. Which version of the server are you using? Todd On Fri, 17 Aug 2001, Steffi Gebauer-Jung wrote: > Hello, > > first time I sent my question in June. > My last email contained it too. > > But anyway. > I found looking for help in the internet, that some people had similar > problems using other programs. > So I thought, that basic properties of the system cause my problems. > > Now I'm using an older version of perl for GeneX, namely 5.6.0 instead of > 5.6.1. > It works fine!!! (Inspite of the status page shows the older version, as for > Genex itself too.) > > Only the feature "Browse Database" does not work and replies with the > message: > Not a valid CGI object at /usr/local/genex/perl5/Bio/Genex/HTMLUtils.pm > line 456. > > Thanks for your response, Steffi > > > > "Todd F. Peterson" wrote: > > > Steffi: > > > > I looked through the list archive and couldn't find your original problem > > report. We would be happy to help you with your problems. Please ask > > again. We are sorry that you did not get a response the first time. > > > > Todd Peterson > > Software Developer > > NCGR > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > |
|
From: Steffi Gebauer-J. <geb...@ic...> - 2001-08-17 15:58:25
|
Hello,
first time I sent my question in June.
My last email contained it too.
But anyway.
I found looking for help in the internet, that some people had similar
problems using other programs.
So I thought, that basic properties of the system cause my problems.
Now I'm using an older version of perl for GeneX, namely 5.6.0 instead of
5.6.1.
It works fine!!! (Inspite of the status page shows the older version, as for
Genex itself too.)
Only the feature "Browse Database" does not work and replies with the
message:
Not a valid CGI object at /usr/local/genex/perl5/Bio/Genex/HTMLUtils.pm
line 456.
Thanks for your response, Steffi
"Todd F. Peterson" wrote:
> Steffi:
>
> I looked through the list archive and couldn't find your original problem
> report. We would be happy to help you with your problems. Please ask
> again. We are sorry that you did not get a response the first time.
>
> Todd Peterson
> Software Developer
> NCGR
|
|
From: Todd F. P. <tf...@nc...> - 2001-08-17 15:53:54
|
The source code is included in the developer versions of the Curation Tool. The developer versions begin with ct150_dev. The developer versions are available for Unix and Windows although the source code it the same. See http://genex.ncgr.org/genex/download/curation_tool The server souce code is included inside of the archive in the form of various Perl files and Unix scripts. Todd On Fri, 17 Aug 2001, Shih-hsiu Lin wrote: > Where can I down load GeneX source code? > > > Shih-Hsiu Lin > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > |
|
From: Todd F. P. <tf...@nc...> - 2001-08-17 15:47:41
|
GeneX communicates with other tools using XML, nga, ngm files produced by the Curation Tool. In many cases, the XML from the Curation Tool is imported into the Postgres Database using XML2DB.pl. Then, the web server has interfaces to some of the analyis tools. The user navigates through the web forms to select and filter the data which the server fetches from the database. See the tutorials at http://genex.ncgr.org. Will research some more on R since I have not used it until recently (the Curation Tool has been my focus). Todd On Fri, 17 Aug 2001, Shih-hsiu Lin wrote: > Todd, > How does GeneX communicate with other applications such as R? I > mean like can I open R from GeneX to perform stat. analysis on experiment > data? Also, how can I use XCluster to work with GeneX? > > > Shih-Hsiu Lin > 10:09am > 8/17/2001 > > > |
|
From: Todd F. P. <tf...@nc...> - 2001-08-17 15:39:20
|
Steffi: I looked through the list archive and couldn't find your original problem report. We would be happy to help you with your problems. Please ask again. We are sorry that you did not get a response the first time. Todd Peterson Software Developer NCGR On Fri, 17 Aug 2001, Steffi Gebauer-Jung wrote: > Hello, > > some weeks ago I sent an email to this list, > asking for some help. Unfortunately it was around > the end of the month, so, if you only look at the > messages of the current month, you possibly did > not see my question. > May I kindly ask you again to give me some hints > for solving my problems? > > Thanks a lot, Steffi > > > --------------------------------------- > > Hello all, > > thanks for the first answer. > > I will attach the content of the Server Status > Page. > The file genex-errors.txt is empty. > > The PostgreSQL version is 7.1-1. > Our operation system is Linux (2.4.2-2). > > While checking why the cgi-scripts don't get any > parameters, I found > that using > enctype="application/x-www-form-urlencoded" > instead of > enctype="multipart/form-data" > seems to solve at least a part of the problem. > > But because I have more recent versions of Perl > and CGI than the NCGR > server has and the enctype originally used is the > modern one, it should > > work too! > > Thanks for your help, Steffi > > > > Here is the content of the "GeneX Server > Installation Status Page": > > GeneX Server Information > > Version Date of Version Installation > Date Installed By > 1.0.2 > 2001-05-02 09:39:47 -0700 > 2001-06-25 17:34:33 > +0200 > > geb...@ic... > > > GeneX Database Information > > Version > Date of Version > Installation Date > Installed By > > Description > > > Perl Information > > Path to Interpreter Version > /usr/local/bin/perl 5.6.1 > > > Perl Module Information > > Module Name Version > Bio::Genex 2.6.1 > Class::ObjectTemplate 0.4 > Class::ObjectTemplate::DB 0.23 > CGI 3.02 > DBI 1.18 > DBD::Pg 1.00 > XML::DOM 1.29 > Term::ReadKey 2.14 > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > |
|
From: Shih-hsiu L. <ma...@jh...> - 2001-08-17 15:16:50
|
Where can I down load GeneX source code? Shih-Hsiu Lin |
|
From: Steffi Gebauer-J. <geb...@ic...> - 2001-08-17 08:38:59
|
Hello,
some weeks ago I sent an email to this list,
asking for some help. Unfortunately it was around
the end of the month, so, if you only look at the
messages of the current month, you possibly did
not see my question.
May I kindly ask you again to give me some hints
for solving my problems?
Thanks a lot, Steffi
---------------------------------------
Hello all,
thanks for the first answer.
I will attach the content of the Server Status
Page.
The file genex-errors.txt is empty.
The PostgreSQL version is 7.1-1.
Our operation system is Linux (2.4.2-2).
While checking why the cgi-scripts don't get any
parameters, I found
that using
enctype="application/x-www-form-urlencoded"
instead of
enctype="multipart/form-data"
seems to solve at least a part of the problem.
But because I have more recent versions of Perl
and CGI than the NCGR
server has and the enctype originally used is the
modern one, it should
work too!
Thanks for your help, Steffi
Here is the content of the "GeneX Server
Installation Status Page":
GeneX Server Information
Version Date of Version Installation
Date Installed By
1.0.2
2001-05-02 09:39:47 -0700
2001-06-25 17:34:33
+0200
geb...@ic...
GeneX Database Information
Version
Date of Version
Installation Date
Installed By
Description
Perl Information
Path to Interpreter Version
/usr/local/bin/perl 5.6.1
Perl Module Information
Module Name Version
Bio::Genex 2.6.1
Class::ObjectTemplate 0.4
Class::ObjectTemplate::DB 0.23
CGI 3.02
DBI 1.18
DBD::Pg 1.00
XML::DOM 1.29
Term::ReadKey 2.14
|
|
From: Todd P. <tf...@nc...> - 2001-08-16 19:38:41
|
The 'SELECT ROW' button is used to link a record to some field in the parent
screen. For example, when you are editing a Hybridization, you must select
an Array Layout. To do this you click the EDIT/VIEW button and the Table
Name: Array Layout screen appears. At this point you may add a row or click
on a row and click 'SELECT ROW'. When 'SELECT ROW' is clicked, the Table
Name: Array Layout screen disappears and the selected Array Layout is
associated with the parent Hybridization. There is a one-to-one relationship
between a Hybridization and an Array Layout...a Hybridization MUST have one
and only one Array Layout.
In the case of the Array Measurement, there is a one-to-many relationship
between the parent Hybridization and the children Array Measurements. One
Array Measurement may belong to only one Hybridization. A Hybridiztion may
have many Array Measurements, though. So, what I'm trying to get to is that
the Table Name: Array Measurement screen is showing the list of Array
Measurements that BELONG to the parent Hybridization. This means they have
already been 'Selected' to be part of the Hybridization by adding them.
That's why there is no SELECT ROW button.
The Experiment/Hybridization/Array Layout/Array Measurement hierarchy in the
curation tool looks like this:
Experiment
|-Hybridization 1
| |-Array Layout-H1
| |-Array Measurement-H1-1 (all Array Measurements are unique)
| |-Array Measurement-H1-2
| |- ....
| |-Array Measurement-H1-n
|
|-Hybridization 2
| |-Array Layout-H2 (Array Layout-H1 could be the same as Array
Layout-H2)
| |-Array Measurement-H2-1
| |-Array Measurement-H2-2
| |- .....
| |-Array Measurement-H2-n
|
|-Hybridization ....
----- Original Message -----
From: "Shih-hsiu Lin" <ma...@jh...>
To: "Todd F. Peterson" <tf...@nc...>
Sent: Thursday, August 16, 2001 12:48 PM
Subject: Bug in Curation Tool 1.50 Unix Version
> Todd,
> In the Curation Tool 1.50 for Unix, the window "Table Name: Array
> Measurements" is missing the "SELECT ROW" button.
>
>
>
> Shih-Hsiu Lin
> 2:47pm
> 8/16/2001
>
>
>
|
|
From: <ja...@op...> - 2001-08-15 19:43:15
|
"Joe Roden" <ro...@ai...> writes: > # $Id: DBI.pm,v 10.25 1999/07/12 02:02:33 timbo Exp $ > # $Id: Pg.pm,v 1.8 1998/09/27 19:12:22 mergl Exp $ Hey Joe, Glad to hear from you. Your modules are badly out of date, and I know that Pg.pm dealt with issues like this last year. jas. # $Id: Pg.pm,v 1.44 2001/06/27 17:54:58 mergl Exp $ # $Id: DBI.pm,v 10.32 2000/06/14 20:04:03 timbo Exp $ |
|
From: Todd F. P. <tf...@nc...> - 2001-08-15 19:32:19
|
try gen...@li... or go to http://sourceforge.net/mail/?group_id=16453 for mailing list archives. congratulations on your successful install. i hope it works well for you. let me know if there are any more problems. todd On Wed, 15 Aug 2001, Shih-hsiu Lin wrote: > Hi Todd, > Sorry to bother you again. I have a question. Is there a web site > that people post their question about GeneX? Something works like a > bulletin board. By the way, I have successfully installed GeneX. Thank for > all your helps. > > > Shih-Hsiu Lin > 3:12pm > 8/15/2001 > > > |
|
From: Joe R. <ro...@ai...> - 2001-08-15 18:54:45
|
Hi Guys,
We in Barbara Wold's lab at Caltech have resumed our interest in
genex and so I've downloaded & installed the latest stable release
(1.0.4), and re-installed our genex database. I've again hit some
DBI & postgres permission issues I'd like your advice on.
If you recall, back in July we had problems with DBI connections
and postgres permissions. At the time you guys suggested we use
unix domain sockets instead of tcp/ip connections to postgress. I
think we *did* have it set then to use unix sockets, as we do today.
On further investigation I think our problems are becoming clearer.
The typical perl scripts that work with the genex database fail. I
have two examples:
- during installation (executed as root) the script to update the
password and contact info failed with a permission denied error.
(We've fixed that by running it as postgres user).
- cgi's such as fetch_table.pl fail due to permission denied errors.
(that's where we were in July) But now we figured out they *work*
if run as the postgres user.
Noticing that success/failure depends on the unix username, I dug in
further and observed that DBI->connect() ignores the user and
password arguments passed to it; instead it falls back to
using the unix username to determine postgres access permissions.
I can get around the DBI->connect() problem by either:
- setting environment the PGUSER environment variable to 'genex'
prior to running such scripts; or
- adding " user=genex" to the connect_string variable that is
passed to connect().
Do you guys have any idea why DBI->connect() ignores the user/password
arguments? Our versions of DBI & Pg (haven't checked if they're totally
recent) are:
# $Id: DBI.pm,v 10.25 1999/07/12 02:02:33 timbo Exp $
# $Id: Pg.pm,v 1.8 1998/09/27 19:12:22 mergl Exp $
Thanks for your advice!
Joe
|
|
From: Todd P. <tf...@nc...> - 2001-08-14 20:20:24
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This didn't make the sourceforge list originally (due to message size) so I'm fwd'g again without the huge attachments. I also meant to say '2 decimal points'; i.e., 1..94E+05 instead of '2 decimal places' in item 2. Todd ----- Original Message ----- From: "Todd Peterson" <tf...@nc...> To: "Rick Tarleton" <tar...@cb...>; <ge...@nc...> Cc: <gen...@li...> Sent: Tuesday, August 14, 2001 10:54 AM Subject: Re: Genex problems > OK...here's what I figured out: > > 1. The sequence feature col file did not have a valid extra-type specified. > 2. The spot measurement file has several floating point values with 2 > decimal places in them. > 3. Line 255 of the layout file has 2 extra columns at the end of the line. > 4. Managed to create an array layout with 4942 user sequence features and > 4942 array layout spots when I did the first array measurement, it got an > error message of many missing values. It did create the measurement, though, > with 4242 spots found. Did verify that the first one it complained about was > not there (id=4033). Have included the Curation Tool output after minimally > marking up 2 data columns. > > Todd Peterson > Software Developer > NCGR > > ----- Original Message ----- > From: "Rick Tarleton" <tar...@cb...> > To: <ge...@nc...> > Sent: Saturday, August 11, 2001 6:24 AM > Subject: Genex problems > > > > Hi: > > > > I have been hammering away at the curation tool on Genex for most of > > this week and can't get it quite figured out - hope you can help. > > > > We have custom glass arrays (mguide arrayer) read on a GMS scanner and > > the data processed through microarray suite to obtain ratios. Genex > > seems to be set up nicely on a Linux machine and I am trying to use the > > curation tool on a windows machine (not a real x-windows fan). > > > > I think my biggest problem is in making the column definition files - I > > thought I had it figured out but apparently not. I am mostly going from > > the test data supplied to figure this out - the tutorial does not help a > > lot there - is there a better help file on how to do this? > > > > Anyway, I seem to be able to get the sequence feature, layout and spot > > measurement data read in OK (it gets validated) but then I get into > > problems. First, in the 'Hybridization and Detection' page, when I > > select 'edit/view' for the 'array layout' line, I get the 'table > > name:array layouts' window which lists the two test data - 'pat brown's > > and the panorama'. When I try to 'add row' to this list, nothing > > happens - likewise if I try to 'use row as template'. I can edit one of > > the existing layouts (mod/view) - which I have done, and proceeded. > > This opens the 'edit array layout information' window. This window > > shows that I have the expected number of 'view user sequence features' > > - in this case 4992 - but the 'view array layout spots' is '0'. If I > > proceed on from this, to the 'edit array measurement' window and then > > try to save the setup, I get a meassage for each of the entries that > > "the selected array does not have an array layout spot for the array > > layout spot ......" > > > > So that is where I am stuck. > > > > I am attaching the data files and the column definition files. The seq > > feature and layout entries are from the 0807.gip file and use the > > arrayDb and layout_gip col def files, respectively. The spot intensity > > file is SI 0807... and uses the 'spot_meas' col def file. > > > > I would appreciate any help or suggestions - particularly any additional > > help files on inputting these data. I like the look of the package so > > far. We have been working on adapting the ArrayDB program from the > > NCHGR for our use so I realize the difficulties involved. > > > > Thanks in advance > > > > Rick Todd Peterson NCGR mailto:tf...@nc... (505) 995-4417 |
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From: Todd F. P. <tf...@nc...> - 2001-08-13 15:29:27
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Dear Ron and Karin: I created a project and got the curation tool running inside of it using JDeveloper from Oracle which is based upon JBuilder. Here is what I used for various paths (my base install dir is f:\ct): source path: f:\ct\java output path: f:\ct\classes working directory: f:\ct\data You must add f:\ct\lib\xerces.jar to the Required Libraries list. The 'main' class is org.ncgr.genex.curator.Curator and should have command line options of -Xmx96m -Xms96m. We usually package the class files in the classes directory using the following sequence: cd f:\ct\classes jar -cf ..\lib\genex.jar org this creates f:\ct\lib\genex.jar so that from the f:\ct\data directory, the following command works to run it: java -Xmx96m -Xms96m -classpath ..\lib\genex.jar;..\lib\xerces.jar org.ncgr.genex.curator.Curator Todd On Sun, 12 Aug 2001, Ron Ophir wrote: > Dear Developer, > I am having a student that programs in java and we would like to add some features to the curation tool which might contribute you. She is currently working on PC in JBuilder, however we would love to hear from you about debugging and developing enviroment on linux. Till we change to linux, she would like to ask the following question: > I can't run or compile (rebuild) the program after creating a project with all the java files. In the attached word document I described the error. I think it's a problem with the configuration of the 'working enviroment'. Please follow the attached file for more details and tell me what you think. > Thanks, > Ron and Karin > |
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From: Ron O. <Ls...@wi...> - 2001-08-12 11:06:45
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Dear Developer, I am having a student that programs in java and we would like to add some = features to the curation tool which might contribute you. She is currently = working on PC in JBuilder, however we would love to hear from you about = debugging and developing enviroment on linux. Till we change to linux, she = would like to ask the following question: I can't run or compile (rebuild) the program after creating a project = with all the java files. In the attached word document I described the = error. I think it's a problem with the configuration of the 'working = enviroment'. Please follow the attached file for more details and tell me = what you think. Thanks, Ron and Karin |
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From: Todd F. P. <tf...@nc...> - 2001-08-11 18:16:06
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Rick: I will take a look at your data and try to see where the problem lies. You are correct in your approach. When we can create a valid Array Layout, we should be in business. Todd Peterson Software Developer NCGR On Sat, 11 Aug 2001, Rick Tarleton wrote: > Hi: > > I have been hammering away at the curation tool on Genex for most of > this week and can't get it quite figured out - hope you can help. > > We have custom glass arrays (mguide arrayer) read on a GMS scanner and > the data processed through microarray suite to obtain ratios. Genex > seems to be set up nicely on a Linux machine and I am trying to use the > curation tool on a windows machine (not a real x-windows fan). > > I think my biggest problem is in making the column definition files - I > thought I had it figured out but apparently not. I am mostly going from > the test data supplied to figure this out - the tutorial does not help a > lot there - is there a better help file on how to do this? > > Anyway, I seem to be able to get the sequence feature, layout and spot > measurement data read in OK (it gets validated) but then I get into > problems. First, in the 'Hybridization and Detection' page, when I > select 'edit/view' for the 'array layout' line, I get the 'table > name:array layouts' window which lists the two test data - 'pat brown's > and the panorama'. When I try to 'add row' to this list, nothing > happens - likewise if I try to 'use row as template'. I can edit one of > the existing layouts (mod/view) - which I have done, and proceeded. > This opens the 'edit array layout information' window. This window > shows that I have the expected number of 'view user sequence features' > - in this case 4992 - but the 'view array layout spots' is '0'. If I > proceed on from this, to the 'edit array measurement' window and then > try to save the setup, I get a meassage for each of the entries that > "the selected array does not have an array layout spot for the array > layout spot ......" > > So that is where I am stuck. > > I am attaching the data files and the column definition files. The seq > feature and layout entries are from the 0807.gip file and use the > arrayDb and layout_gip col def files, respectively. The spot intensity > file is SI 0807... and uses the 'spot_meas' col def file. > > I would appreciate any help or suggestions - particularly any additional > help files on inputting these data. I like the look of the package so > far. We have been working on adapting the ArrayDB program from the > NCHGR for our use so I realize the difficulties involved. > > Thanks in advance > > Rick > |
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From: Todd P. <tf...@nc...> - 2001-08-10 21:23:17
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use test/test for user/pw. Todd ----- Original Message ----- From: "Shih-hsiu Lin" <ma...@jh...> To: <gen...@li...> Sent: Friday, August 10, 2001 3:00 PM Subject: [GeneX-dev] Question about Using Curation Tool > To whom it may concert, > On the Curation Tool, I clicked "CREATE NEW EXPERIMENT SET", then > clicked on "DOWNLOAD CONTROL FILES". Then the brower opened a web page > that required login name and password. I wonder how I can register an > account. Thank you. > > > Sincerely, > > Shih-Hsiu Lin > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > > |
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From: Todd P. <tf...@nc...> - 2001-08-10 21:22:08
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Took a look at java.sun.com and searched for /usr/bin/cut and found this (http://java.sun.com/products/help/installation-help.html): Linux: Getting started Many customers have written in about J2SE v1.3 on Linux RedHat v7.1. Our Linux guru says: ******** Two things they can do are: 1) upgrade to the J2SE SDK v1.3.1rc2 or later (URL requires login to the JDC - a free service) 2) set LD_ASSUME_KERNEL=2.2.5 in their shell (add that line in go.sh) environment and link /usr/bin/cut to /bin/cut (ln -s /bin/cut /usr/bin/cut) ******** Related links to Java technology on the Linux Platform: a.. The article "A Guide to Getting Started" gives Installation tips b.. Resource Page ----- Original Message ----- From: "Shih-hsiu Lin" <ma...@jh...> To: "Todd Peterson" <tf...@nc...> Sent: Friday, August 10, 2001 12:26 PM Subject: GeneX Installation Problems > Todd, > Sorry to bother you again. I sent an email to the address you gave > me, but I still haven't received respond yet. Thus, I send this email to > ask you for help. > I am installing the Curation Tool. I ran the following command > > sh go.sh > > but I got the following error message: > > ../jre1.3.0/bin/java: /usr/bin/cut: No such file or directory > /usr/local/src/ct100_usrlnx/jre1.3.0/bin/i386/native_threads/java: error > while loading shared libraries: libjvm.so: cannot load shared object file: > No such file or directory > > Please give me some suggestions. Thank you. > > > Matt > 2:24pm > 8/10/2001 > > > |
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From: Todd P. <tf...@nc...> - 2001-08-10 21:16:54
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It looks like java calls an OS utility called cut which should reside in /usr/bin. It must use this to figure out where the shared library is since there are 3 versions of libjvm.so which are located in different directories under hre1.3.0/bin/i386. So, to fix the problem, the file /usr/bin/cut must be present. I have included the version of cut from one of our linux machines. To locate it on your machine, type: find / -name cut Let me know if that doesn't help. I must have given you the wrong sourceforge address, so I have cc'd once more the list. thanks, todd ----- Original Message ----- From: "Shih-hsiu Lin" <ma...@jh...> To: "Todd Peterson" <tf...@nc...> Sent: Friday, August 10, 2001 12:26 PM Subject: GeneX Installation Problems > Todd, > Sorry to bother you again. I sent an email to the address you gave > me, but I still haven't received respond yet. Thus, I send this email to > ask you for help. > I am installing the Curation Tool. I ran the following command > > sh go.sh > > but I got the following error message: > > ../jre1.3.0/bin/java: /usr/bin/cut: No such file or directory > /usr/local/src/ct100_usrlnx/jre1.3.0/bin/i386/native_threads/java: error > while loading shared libraries: libjvm.so: cannot load shared object file: > No such file or directory > > Please give me some suggestions. Thank you. > > > Matt > 2:24pm > 8/10/2001 > > > |
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