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From: Harry M. <man...@ho...> - 2001-07-03 16:38:44
|
Hi Smita, That's great! Would you mind sending us the modifications you had to make to do this? We are thinking of porting the entire platform to Win2k and this would be one thing we wouldn;t have to do. Re: having treeview be launched automatically, I don;t know as we haven;t started work on the port yet. Are you using the Cygwin package or using it native with NT services? Smita Mitra wrote: > > Dear Harry, > > I have modified your xcluster_handler.pl and > xcluster_form.pl programs for my winNT system to talk > to xcluster and they have worked well for me. Thanks a > lot! I would now like to have the .cdt file generated > by xcluster to be passed on to TreeView via cmdline to > generate a graphical output. Treeview from cmdline > seems to start the application and does not take any > input file over cmdline. Have you worked on this at > all? > > Thanks a lot for your help. > Smita. > > __________________________________________________ > Do You Yahoo!? > Get personalized email addresses from Yahoo! Mail > http://personal.mail.yahoo.com/ -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
|
From: Stephen J. <bla...@ix...> - 2001-07-02 16:17:16
|
Greg-- can you remove me (or tell me how I can remove myself) from the GeneX
newsgroup(s). Thanks, Steve Joseph
----- Original Message -----
From: Greg D. Colello <gd...@nc...>
To: <gen...@li...>
Sent: Monday, July 02, 2001 9:19 AM
Subject: Re: [GeneX-dev] Curation tool bug report
> Ron:
>
> This is quite a nice list of problems (if problems are ever nice).
Actually it's
> nice that you spent so much time cataloging these problems.
>
> It would be helpful to me if I had a copy of your complete XML output. The
best
> way to accomplish this is to ftp the .jar version that was submitted to
the
> server. If you have an anonymous ftp server, then put it there and give me
> instructions on how to retrieve. Otherwise I will have to create an ftp
account
> for you here.
>
> I have completed work on the latest set of improvements to the Curation
Tool,
> and I can focus on these problems. I need to determine whether these
problems
> exist in the current code. If so, I will fix them. In any case it looks
like I
> will need to post a new version of the Curation Tool.
>
> Greg
>
> >From: "Ron Ophir" <Ls...@wi...>
> >To: <gen...@li...>
> >Mime-Version: 1.0
> >Subject: [GeneX-dev] Curation tool bug report
> >Date: Mon, 02 Jul 2001 14:01:22 +0300
> >
> >Dear Greg D. Colello,
> >
> >I am sending a bug report for the xml file as it is generated by the
curation
> tool. The report is based on the minimum input request as it appears by
the
> high-lighted fields. In other words, speaking I followed the yellow guide
using
> the tes data provided by GeneX.
> > Here is my entry path:
> >New Experiment set:
> > Experiment set data file
> > Required:
> >Array layout
> >Sequence feature
> >Array measurement
> >One2Many: File information Edit
> > Required:
> > GeneX use
> > File name
> >Files default species
> > Edit Experiment set
> > Required:
> > Name
> > Data supplier
> >Treatment type
> >One2Many: Hybridization and detection
> > Required
> > ArrayLayout
> > Required
> > Name
> >One2Many: ArrayMeasurments
> > Required
> > Sample
> > Required:
> > Sample name
> > Species
> > Organism supplier
> > Channel
> > Type
> >Data File ColName
> >Here are XML file bugs:
> >
> >Under <external_file_list> always appears null attribute <
external_file/> and
> cause
> >The following error:
> >Can't call method "getValue" on an undefined value at ./xml2db.pl line
1548.
> >
> >After fixing this bug I got:
> >
> >Background:
> >
> >Adding a New arraylayout which required only name which I put the value
"New".
> >Causing error message:
> >7ArrayLayout: SELECT al_pk from ArrayLayout where name = 'New' AND at
> ./xml2db.pl line 1650.
> >
> >Possible solution:
> >
> >It seemes that contact_id and technology_type are required as well.
> >
> >After fixing this bug I got:
> >
> >DBD::Pg::db do failed: ERROR: ExecAppend: Fail to add null value in not
null
> attribute biology_description at ./xml2db.pl line 1603.
> >7ExperimentSet: INSERT INTO ExperimentSet (release_date, treatment_type,
> submission_date, name, us_fk, is_public, group_can_update,
quantity_series_type)
> VALUES ('May 31, 2000', 'developmental_stage_comparison', 'Jul 1, 2001',
> 'WisExp', '0', '0', '0', '<not-applicable>') at ./xml2db.pl line 1603.
> >
> >Possible solution:
> >
> ><experiment_set
> > id="CTXML:207" owner_contact_id="CTXML:69" name="WisExp"
> > is_public="0" group_can_update="0"
> > treatment_type="developmental_stage_comparison"
> > quantity_series_type="<not-applicable>"
> >
> >adding this line in the xml file:
> > biology_description="biological experiment"
> >
> > release_date="May 31, 2000"
> > submission_date="Jul 1, 2001">
> >After fixing this bug I got:
> >DBD::Pg::db do failed: ERROR: ExecAppend: Fail to add null value in not
null
> attribute submission_date at ./xml2db.pl line 1603.
> >7ArrayMeasurement: INSERT INTO ArrayMeasurement (release_date,
description,
> file_name, name, group_can_update, is_public, experiment_date, type,
> primary_es_fk, column_name, spot_measurement_units, hybridization_name,
al_fk,
> channel_name, smp_fk) VALUES ('May 31, 2000', 'hjhkjhlkjh',
> 'E:\Downloads\Curation Tools\ct101_usrwin\data\testdata\arraymeas.txt',
> 'IH100_Rep1_Filter_1_Exp_1', '0', '0', 'May 30, 2000', 'background', '36',
> 'IH100 Rep1 Filter 1 Exp 1', '<not-applicable>', 'H&DWis', '19', 'cy3',
'50')
> at ./xml2db.pl line 1603.
> >
> >In the "Hybridization & Detection" screen there was no place to put
submission
> date which was then not added to the ArrayMeasurement at the XML file.
Therefore
> I added this:
> ><array_measurement
> > id="CTXML:208" type="background"
> >this line was added:
> > submission_date="Jul 1, 2001"
> >
> > name="IH100_Rep1_Filter_1_Exp_1"
> > sample_id="CTXML:201" channel_id="CTXML:209"
> > file_name="E:\Downloads\Curation
> Tools\ct101_usrwin\data\testdata\arraymeas.txt"
> > column_name="IH100 Rep1 Filter 1 Exp 1" >
> >
> >And then I got the following message:
> >Your data has been successfully entered into the database.
> >I hope you'll find it usefull, Greg
> >and thanks for the help,
> >Ron
> >
> >
> >
> >
> >
>
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
|
|
From: Greg D. C. <gd...@nc...> - 2001-07-02 15:20:56
|
Ron:
This is quite a nice list of problems (if problems are ever nice). Actually it's
nice that you spent so much time cataloging these problems.
It would be helpful to me if I had a copy of your complete XML output. The best
way to accomplish this is to ftp the .jar version that was submitted to the
server. If you have an anonymous ftp server, then put it there and give me
instructions on how to retrieve. Otherwise I will have to create an ftp account
for you here.
I have completed work on the latest set of improvements to the Curation Tool,
and I can focus on these problems. I need to determine whether these problems
exist in the current code. If so, I will fix them. In any case it looks like I
will need to post a new version of the Curation Tool.
Greg
>From: "Ron Ophir" <Ls...@wi...>
>To: <gen...@li...>
>Mime-Version: 1.0
>Subject: [GeneX-dev] Curation tool bug report
>Date: Mon, 02 Jul 2001 14:01:22 +0300
>
>Dear Greg D. Colello,
>
>I am sending a bug report for the xml file as it is generated by the curation
tool. The report is based on the minimum input request as it appears by the
high-lighted fields. In other words, speaking I followed the yellow guide using
the tes data provided by GeneX.
> Here is my entry path:
>New Experiment set:
> Experiment set data file
> Required:
>Array layout
>Sequence feature
>Array measurement
>One2Many: File information Edit
> Required:
> GeneX use
> File name
>Files default species
> Edit Experiment set
> Required:
> Name
> Data supplier
>Treatment type
>One2Many: Hybridization and detection
> Required
> ArrayLayout
> Required
> Name
>One2Many: ArrayMeasurments
> Required
> Sample
> Required:
> Sample name
> Species
> Organism supplier
> Channel
> Type
>Data File ColName
>Here are XML file bugs:
>
>Under <external_file_list> always appears null attribute < external_file/> and
cause
>The following error:
>Can't call method "getValue" on an undefined value at ./xml2db.pl line 1548.
>
>After fixing this bug I got:
>
>Background:
>
>Adding a New arraylayout which required only name which I put the value "New".
>Causing error message:
>7ArrayLayout: SELECT al_pk from ArrayLayout where name = 'New' AND at
./xml2db.pl line 1650.
>
>Possible solution:
>
>It seemes that contact_id and technology_type are required as well.
>
>After fixing this bug I got:
>
>DBD::Pg::db do failed: ERROR: ExecAppend: Fail to add null value in not null
attribute biology_description at ./xml2db.pl line 1603.
>7ExperimentSet: INSERT INTO ExperimentSet (release_date, treatment_type,
submission_date, name, us_fk, is_public, group_can_update, quantity_series_type)
VALUES ('May 31, 2000', 'developmental_stage_comparison', 'Jul 1, 2001',
'WisExp', '0', '0', '0', '<not-applicable>') at ./xml2db.pl line 1603.
>
>Possible solution:
>
><experiment_set
> id="CTXML:207" owner_contact_id="CTXML:69" name="WisExp"
> is_public="0" group_can_update="0"
> treatment_type="developmental_stage_comparison"
> quantity_series_type="<not-applicable>"
>
>adding this line in the xml file:
> biology_description="biological experiment"
>
> release_date="May 31, 2000"
> submission_date="Jul 1, 2001">
>After fixing this bug I got:
>DBD::Pg::db do failed: ERROR: ExecAppend: Fail to add null value in not null
attribute submission_date at ./xml2db.pl line 1603.
>7ArrayMeasurement: INSERT INTO ArrayMeasurement (release_date, description,
file_name, name, group_can_update, is_public, experiment_date, type,
primary_es_fk, column_name, spot_measurement_units, hybridization_name, al_fk,
channel_name, smp_fk) VALUES ('May 31, 2000', 'hjhkjhlkjh',
'E:\Downloads\Curation Tools\ct101_usrwin\data\testdata\arraymeas.txt',
'IH100_Rep1_Filter_1_Exp_1', '0', '0', 'May 30, 2000', 'background', '36',
'IH100 Rep1 Filter 1 Exp 1', '<not-applicable>', 'H&DWis', '19', 'cy3', '50')
at ./xml2db.pl line 1603.
>
>In the "Hybridization & Detection" screen there was no place to put submission
date which was then not added to the ArrayMeasurement at the XML file. Therefore
I added this:
><array_measurement
> id="CTXML:208" type="background"
>this line was added:
> submission_date="Jul 1, 2001"
>
> name="IH100_Rep1_Filter_1_Exp_1"
> sample_id="CTXML:201" channel_id="CTXML:209"
> file_name="E:\Downloads\Curation
Tools\ct101_usrwin\data\testdata\arraymeas.txt"
> column_name="IH100 Rep1 Filter 1 Exp 1" >
>
>And then I got the following message:
>Your data has been successfully entered into the database.
>I hope you'll find it usefull, Greg
>and thanks for the help,
>Ron
>
>
>
>
>
|
|
From: Ron O. <Ls...@wi...> - 2001-07-02 11:01:51
|
Dear Greg D. Colello,
I am sending a bug report for the xml file as it is generated by the =
curation tool. The report is based on the minimum input request as it =
appears by the high-lighted fields. In other words, speaking I followed =
the yellow guide using the tes data provided by GeneX.
Here is my entry path:
New Experiment set:
Experiment set data file
Required:=20
Array layout
Sequence feature
Array measurement
One2Many: File information Edit
Required:
GeneX use
File name
Files default species
Edit Experiment set
Required:
Name
Data supplier
Treatment type
One2Many: Hybridization and detection
Required
ArrayLayout
Required
Name
One2Many: ArrayMeasurments
Required
Sample
Required:
Sample name
Species
Organism supplier
Channel
Type
Data File ColName
Here are XML file bugs:
=20
Under <external_file_list> always appears null attribute < external_file/> =
and cause
The following error:
Can't call method "getValue" on an undefined value at ./xml2db.pl line =
1548.
=20
After fixing this bug I got:
=20
Background:
=20
Adding a New arraylayout which required only name which I put the value =
"New".
Causing error message:
7ArrayLayout: SELECT al_pk from ArrayLayout where name =3D 'New' AND at =
./xml2db.pl line 1650.=20
=20
Possible solution:
=20
It seemes that contact_id and technology_type are required as well.
=20
After fixing this bug I got:
=20
DBD::Pg::db do failed: ERROR: ExecAppend: Fail to add null value in not =
null attribute biology_description at ./xml2db.pl line 1603.
7ExperimentSet: INSERT INTO ExperimentSet (release_date, treatment_type, =
submission_date, name, us_fk, is_public, group_can_update, quantity_series_=
type) VALUES ('May 31, 2000', 'developmental_stage_comparison', 'Jul 1, =
2001', 'WisExp', '0', '0', '0', '<not-applicable>') at ./xml2db.pl line =
1603.
=20
Possible solution:
=20
<experiment_set
id=3D"CTXML:207" owner_contact_id=3D"CTXML:69" name=3D"WisExp"
is_public=3D"0" group_can_update=3D"0"
treatment_type=3D"developmental_stage_comparison"
quantity_series_type=3D"<not-applicable>"
=20
adding this line in the xml file:
biology_description=3D"biological experiment"
=20
release_date=3D"May 31, 2000"
submission_date=3D"Jul 1, 2001">
After fixing this bug I got:
DBD::Pg::db do failed: ERROR: ExecAppend: Fail to add null value in not =
null attribute submission_date at ./xml2db.pl line 1603.
7ArrayMeasurement: INSERT INTO ArrayMeasurement (release_date, description,=
file_name, name, group_can_update, is_public, experiment_date, type, =
primary_es_fk, column_name, spot_measurement_units, hybridization_name, =
al_fk, channel_name, smp_fk) VALUES ('May 31, 2000', 'hjhkjhlkjh', =
'E:\Downloads\Curation Tools\ct101_usrwin\data\testdata\arraymeas.txt', =
'IH100_Rep1_Filter_1_Exp_1', '0', '0', 'May 30, 2000', 'background', '36', =
'IH100 Rep1 Filter 1 Exp 1', '<not-applicable>', 'H&DWis', '19', 'cy3', =
'50') at ./xml2db.pl line 1603. =20
=20
In the "Hybridization & Detection" screen there was no place to put =
submission date which was then not added to the ArrayMeasurement at the =
XML file. Therefore I added this:
<array_measurement
id=3D"CTXML:208" type=3D"background"
this line was added:
submission_date=3D"Jul 1, 2001"
=20
name=3D"IH100_Rep1_Filter_1_Exp_1"
sample_id=3D"CTXML:201" channel_id=3D"CTXML:209"
file_name=3D"E:\Downloads\Curation Tools\ct101_usrwin\d=
ata\testdata\arraymeas.txt"
column_name=3D"IH100 Rep1 Filter 1 Exp 1" >
=20
And then I got the following message:
Your data has been successfully entered into the database.
I hope you'll find it usefull, Greg=20
and thanks for the help,
Ron
=20
=20
=20
=20
=20
|
|
From: Greg D. C. <gd...@nc...> - 2001-06-28 15:57:14
|
To all: I am back from trip. I will investigate this. I should be able to reproduce. Greg Colello NCGR > >Here is the error: > > <external_file_list> > <external_file > id="usf_file" > file_name="MySecond_USF_1.ext"/> > <external_file/> > ^^^^^^^^^^^^^^^^ > > <external_file > id="alfile1" > file_name="MySecond_ALS_1.ext"/> > <external_file > id="alfile2" > file_name="MySecond_ALS_2.ext"/> > <external_file > id="amfile1" > file_name="MySecond_AMS_1.ext"/> > </external_file_list> > >Notice the empty <external_file/>. The curation_tool has botched this >up somehow. When I delete this from the XML file it seems to progress >smoothly. Sorry to make you edit this by hand, but I don't know why >the CT generated a bogus file. |
|
From: Steffi Gebauer-J. <geb...@ic...> - 2001-06-27 14:01:07
|
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: Harry M. <man...@ho...> - 2001-06-27 13:14:05
|
I caught this just as I was leaving; could someone please help? Steffi, you'll only get further answers if you send you messages to: gen...@li... as I'm leaving for several days. hjm Steffi Gebauer-Jung wrote: > > Hello, > > thanks for your first answer. > > I will attach the content of the Server Status Page and the > Option.Reminders file. > 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 ond CGI than the NCGR > server has and the enctype originally used is the modern one, it should > work too! > > Thanks for your help, Steffi > > PS: Sorry, for using your personal email. > I will post this message to the mailing list too, but without > the possibly more sensitive Option.Reminders data. > > 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 > > And here follows the content of the Option.Reminders file: > > Following are the Directory and URLs you set or allowed to be set: > CGIDIR = /usr/local/genex/cgi-bin > CGITMPDIR = /tmp/genex > CGITMPURL = http://mint.ice.mpg.de/genex/tmp > CGI_ROOT_URL = http://mint.ice.mpg.de/cgi-bin > CONTACT_EMAIL = geb...@ic... > CURA_TOOL = genex/curation-tool > CYBERT_DIR = genex/cybert > CyberT_Demo_DIR = genex/CyberT-Demo > DB_NAME = genex > DOWNLOAD_DIR = genex/download > DTD2HTML = /usr/bin/dtd2html > DTD_DIR = genex/DTD > DTD_HTML_DIR = /usr/local/genex/lib/dtd/genexml-html > DTD_HTML_URL = http://mint.ice.mpg.de/genex/DTD/genexml-html > ENV_HOME = /tmp/genex > GENEXML_DIR = /usr/local/genex/lib/dtd > GENEXML_URL = http://mint.ice.mpg.de/genex/DTD > GENEX_CACHE_DIR = /usr/local/genex/cache > GENEX_CB_CACHE_DIR = /usr/local/genex/cache/db2xml/cb > GENEX_CGIDIR = /usr/local/genex/cgi-bin/genex > GENEX_CGI_URL = http://mint.ice.mpg.de/cgi-bin/genex > GENEX_CONNECT = $Bio::Genex::LOCAL = 1; > GENEX_CURATOR = geb...@ic... > GENEX_CUR_TOOL_DIR = /usr/local/genex/cgi-bin/genex/curation-tool > GENEX_DBMS = Pg > GENEX_DB_USERSEC = geL8TEYU5FBEI > GENEX_DIR = genex > GENEX_EXAMPLE_DIR = /usr/local/genex/cgi-bin/genex/samples > GENEX_EXP_CACHE_DIR = /usr/local/genex/cache/db2xml/exp > GENEX_EXTRALIBS = use lib q[/usr/local/genex/perl5]; > use lib q[/usr/local/genex/perl5]; > > GENEX_GRAPHICS_URL = http://mint.ice.mpg.de/genex/graphics > GENEX_HOST = localhost > GENEX_HTM_URL = http://mint.ice.mpg.de/genex > GENEX_INSTALLSITE = /usr/local/genex/perl5 > GENEX_LOCAL = 1 > GENEX_MAN1 = /usr/local/genex/man/man1 > GENEX_MAN3 = /usr/local/genex/man/man3 > GENEX_PORT = 5432 > GENEX_QUERY_DIR = /usr/local/genex/cgi-bin/genex/gxquery > GENEX_RO_PASSWORD = readonly > GENEX_RO_USER = readonly > GENEX_SECRET = Mon Jun 25 17:34:24 2001 > GENEX_SERVER_INSTALLED_BY = geb...@ic... > GENEX_SUBMISSION_HOME = /usr/local/genex/submission > GENEX_SU_PASSWORD = genex > GENEX_SU_USER = genex > GENEX_URL_CUR_TOOL = http://mint.ice.mpg.de/cgi-bin/genex/curation-tool > GENEX_URL_EXAMPLE = http://mint.ice.mpg.de/cgi-bin/genex/samples > GENEX_URL_QUERY = http://mint.ice.mpg.de/cgi-bin/genex/gxquery > GNUCUT = /bin/cut > GNUINSTALL = /usr/bin/install > GNUMKDIR = /bin/mkdir > GNUSORT = /bin/sort > GNUTAIL = /usr/bin/tail > GNUTAR = /bin/tar > GRAPHICS_DIR = genex/graphics > GS = /usr/bin/gs > GXQUERY_DIR = genex/gxquery > HTMLDIR = /usr/local/genex/html > HTMLTMPDIR = /usr/local/genex/html/genex/tmp > HTML_ROOT_URL = http://mint.ice.mpg.de > HTTP_ERR_LOG = /var/log/httpd/error_log > INCLUDE_DIR = genex/include > JAR = /usr/java/jdk1.3.1/bin/jar > LOCAL_BIN = /usr/local/genex/bin > LOCAL_LIB = /usr/local/genex/lib > LOCAL_ROOT = /usr/local/genex > LOCAL_SHARE = /usr/local/genex/share > LOCAL_VAR = /usr/local/genex/var > LOGIN_DIR = genex/login > MAX_SYSTMP_SIZE = 100 > MAX_TMPFILE_AGE = 24 > MERGEM_DIR = genex/mergem > MPAGE = /usr/bin/mpage > PATH = .... > PREFIX = /usr/local/genex/perl5 > R = /usr/bin/R > RCLUSTER_PERL_LIB = /usr/local/genex/perl5/RCluster > RCLUST_DIR = genex/rcluster > RCluster_Demo_DIR = genex/RCluster-Demo > R_VERSION = R 1.2.3 (2001-04-26). > SENDMAIL = /usr/sbin/sendmail > START_PERL = #!/usr/local/bin/perl > SYSTMP = /tmp/genex > TOP_LEVEL_DIR = genex/top_level > VERSION_STRING = $Id: install-all.pl,v 1.84.2.6 2001/06/05 00:08:36 hjm > Exp $ > VNCSERVER = /usr/bin/vncserver > WWWHOST = mint.ice.mpg.de > XCLUSTER = /usr/bin/xcluster > XCLUSTER_DIR = genex/xcluster > XGOBI = /usr/bin/xgobi > XGOBID = /usr/bin > XGVIS = /usr/bin/xgvis > XML_WRITER = /usr/local/genex/bin/db2xml.pl > > Following are the Application Paths you set or allowed to be set: > R = /usr/bin/R > cut = /bin/cut > dtd2html = /usr/bin/dtd2html > gs = /usr/bin/gs > install = /usr/bin/install > jar = /usr/java/jdk1.3.1/bin/jar > mkdir = /bin/mkdir > mpage = /usr/bin/mpage > sendmail = /usr/sbin/sendmail > sort = /bin/sort > tail = /usr/bin/tail > tar = /bin/tar > vncserver = /usr/bin/vncserver > xcluster = /usr/bin/xcluster > xgobi = /usr/bin/xgobi > xgvis = /usr/bin/xgvis > > Following are the ENVIRONMENT VARIABLES you set or allowed to be set: > ENV_HOME = /tmp/genex > PATH = > /usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/sda7/genome/bin:/home/steffi/bin:.:/home/steffi/stargate/cpgms:/home/steffi/stargate/pgms:/home/steffi/stargate/pgms1999:/home/steffi/stargate/pgmsold_refresh:/home/steffi/stargate/pgmsold:/home/twiehe/Comptools99:/home/steffi/useful:/opt/jdk1.2/bin:/usr/local/genome/bin > > XGOBID = /usr/bin -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Harry M. <man...@ho...> - 2001-06-27 03:30:09
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Michael Pear wrote: > > We're looking for significant differences in ratios for a treatment by > comparing replicated treatment vs. control slides with control vs control. For > each level, we have 4 replicate slides. All duplicate spots within slides(in-slide replicates) have > been > resolved to means prior to the comparison. If I understand this, one set of ratios (these are 2-color glass slides, no?) is coming from the C vs T and another is coming from C vs C? If this is right, then you should be using the Paired CyberT for the C vs T and run it again with the C vs C to assure yourself that the controls are showing something beyond noise. The C+E form is for Affymetrix-type experiments where the values have been extracted from different slides (the values are not paried.) > We want to judge significance based upon comparison of the log ratios from each set of slides. > I'm wondering what the boundaries are for applying CyberT for this analysis. Going into CyberT, > besides the label column, I have 4 columns each of the ratios for treatment vs. control and control > vs. control. I rely on CyberT for the log transform of these ratios. > > 1) I am assuming that the unpaired C+E analysis is appropriate in this case...there is no > inherent pairing between the slide sets. Correct? Hmm - you're using 2 color glass slides? There IS inherent pairing (If I'm following you correctly) as the C and T have been generated from the same slide. Cybert DOESN'T include support for exactly the experiment that you describe, where C vs C is compared with C vs T. It supposes that you have a series of replicates of C vs T and does t-tests on the replicates (assisted by teh Bayes thingie). But you can run the C vs C slides in the same way to gain confidence that the C vs T show a real change (or use that data to increase the replicates for the C value (altho this is not quite kosher as they will have been generated from a different slide and thus not be paired. > 2) Is use of the Bayesian estimate appropriate for this case? As it relies the assumption of similar > expression levels having similar measurement errors, and we're dealing with (unpaired) ratios, is > using the Bayesian stats incorrect? The Bayesian is appropriate for each test, given the experiment. The t-test assumes homogenous sampling of course, but the Bayesian can be thought of as a data-smoother, sampling areound each sample within each distribution to build up a better estimate of true variance. Again, it doesn't address the model that you have exactly. > 3) If the Bayesian estimate requires expression levels, is there anyway to to supply this to the > unpaired C+E calculation? Yes, if you're using paired data, there is a estimate that you can use that's described in the CyberT Help: http://genomics.biochem.uci.edu/genex/cybert/CTHelp.html#PairedExprCol I'm leaving tomorrow moring for several days so I won't be able to clarify this anymore. You should contact Tony Long for more explicit advice on this; I'm forwarding this to him so he can follow the conversation if necessary. -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Michael P. <mic...@ho...> - 2001-06-27 02:52:36
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We're looking for significant differences in ratios for a treatment by comparing replicated treatment vs. control slides with control vs control. For each level, we have 4 replicate slides. All duplicate spots within slides(in-slide replicates) have been resolved to means prior to the comparison. We want to judge significance based upon comparison of the log ratios from each set of slides. I'm wondering what the boundaries are for applying CyberT for this analysis. Going into CyberT, besides the label column, I have 4 columns each of the ratios for treatment vs. control and control vs. control. I rely on CyberT for the log transform of these ratios. 1) I am assuming that the unpaired C+E analysis is appropriate in this case...there is no inherent pairing between the slide sets. Correct? 2) Is use of the Bayesian estimate appropriate for this case? As it relies the assumption of similar expression levels having similar measurement errors, and we're dealing with (unpaired) ratios, is using the Bayesian stats incorrect? 3) If the Bayesian estimate requires expression levels, is there anyway to to supply this to the unpaired C+E calculation? Regards, Michael Pear |
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From: Harry M. <man...@ho...> - 2001-06-26 20:47:25
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Hi Steffi, Steffi Gebauer-Jung wrote: > After installing all these neccessary software packages and modules I > installed version 1.0.3 first. > Because this did not work and I realized that there was a newer version > available, I tried to install that version (1.0.4). Good! That's the most recent version.. > First I wondered about the server status page, which displayed version > 1.0.2 and no database information at all. The version information is set with a hard-coded number (which should be changed) and is wrong. The incomplete database information is a bit odd, although we have heard of this happeing before as well. Could you send us these files: Option.Reminders genex-errors.txt and also tell us 1) what version of PostgreSQL you are running 2) Operating system and version (output of uname -a) If you can allow us to connect to the database web server by http, we may also be able to gain more information, but don't do so if this is a security risk. Also, please respond to the genex list serv <gen...@li...> as you'll be able to get more to listen to you (and I'll be offline for the next week). harry > Later on I found some broken links, for instance > http://www.ncgr.org/research/genex/schema.html (via "background", > "GeneX data format and model"). This is a result of an update of the NCGR web server, but we'll look into trying to track all those down and edit inthe correct ones. > > But the real problem is, that I cannot use the programs. > So if I try to start RCluster - Hierarchical Clustering - using the > example data "Brown", together with the "Average" agglomeration method > and stop depth 10, I get the following error message: > No service defined at > /usr/local/genex/perl5/RCluster/Utils.pm line 34. > > If I try to query the database (via "Analysis/Query", "Database Query") > by clicking, for instance, on an experiment name, I get the message: > Nothing to filter or select on - please go back and choose > at least one selection! > > But both works well on the server at NCGR, using the same browser. > So it must be any mis-configuration, inspite of an empty > genex-errors.txt file. > > I used /usr/local as LOCAL_ROOT. So I had to add some links, which seem > OK because web sites are to be seen via browser, > and perl scripts are executed, but without or with wrong parameters. > > Because I'm quite new to such installation stuff, I would be happy to > get some hints, how to get GeneX running. > > Thanks a lot in advance, > St. Gebauer-Jung > > What I did: > [postgres@mint GeneX-Server-1.0.4]$ dropdb genex > DROP DATABASE > [postgres@mint GeneX-Server-1.0.4]$ createdb genex > CREATE DATABASE > [postgres@mint GeneX-Server-1.0.4]$ ./init-dump.pl > ....... > Installing the DB dump. This will take a few minutes > > Hit [Enter] to proceed > You are now connected as new user genex. > CREATE > nextval > --------- > 12932 > (1 row) > > CHANGE > CHANGE > ...... > > Congratulations!! You now have a functioning GeneX DB > > [postgres@mint GeneX-Server-1.0.4]$ psql -U readonly genex > genex=> \d > List of relations > Name | Type | Owner > --------------------------------+----------+------- > al_coating | table | genex > al_defaultspotconcunits | table | genex > al_identifiercode | table | genex > al_medium | table | genex > al_spots | table | genex > al_spots_als_pk_seq | sequence | genex > al_technologytype | table | genex > als_spottype | table | genex > am_equationtype | table | genex > am_factorvalues | table | genex > am_spotmeasurementunits | table | genex > am_spots | table | genex > am_spots_ams_pk_seq | sequence | genex > am_suspectspots | table | genex > am_type | table | genex > arraylayout | table | genex > arraylayout_al_pk_seq | sequence | genex > arraymeasurement | table | genex > arraymeasurement_am_pk_seq | sequence | genex > blasthits | table | genex > blasthits_bh_pk_seq | sequence | genex > chromosome | table | genex > chromosome_chr_pk_seq | sequence | genex > citation | table | genex > citation_cit_pk_seq | sequence | genex > contact | table | genex > contact_con_pk_seq | sequence | genex > contacttype | table | genex > ef_majorcategory | table | genex > ef_minorcategory | table | genex > es_quantityseriestype | table | genex > es_treatmenttype | table | genex > experimentfactors | table | genex > experimentfactors_ef_pk_seq | sequence | genex > experimentset | table | genex > experimentset_es_pk_seq | sequence | genex > externaldatabase | table | genex > genexadmin | table | genex > genexadmin_ga_pk_seq | sequence | genex > grouplink | table | genex > groupsec | table | genex > groupsec_gs_pk_seq | sequence | genex > hotspots | table | genex > hs_thresholdtype | table | genex > pga_forms | table | genex > genex=> \q > > [root@mint GeneX-Server-1.0.4]# /usr/local/bin/perl install-all.pl > --SLOW > ..... > Whew!! Time to point your browser at: > .... -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: <ja...@op...> - 2001-06-21 02:21:36
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"Daniel E Sabath" <dsabath@u.washington.edu> writes: > On Tuesday, June 19, 2001, at 08:04 AM, Harry Mangalam wrote: > > I should add that I had previously installed a lot of ported unix apps > and libraries using Fink (see <http://fink.sourceforge.net>), and > perhaps I have some things on my system needed for xgobi that a > standard MacOS X/Darwin installation is missing. That's a useful link for MacOS X folks. Thanks. Harry, maybe we can include a note about it in the INSTALL for OS X people... jas. |
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From: Daniel E S. <dsabath@u.washington.edu> - 2001-06-20 23:41:47
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On Tuesday, June 19, 2001, at 08:04 AM, Harry Mangalam wrote: [some problems with xgobi snipped] > Maybe Dan (Daniel E Sabath <dsabath@u.washington.edu>), who has > gotten GeneX running on his OSX can comment? I had no trouble compiling xgobi using xmkmf > make. It looks like the person having trouble had library issues, but I don't know enough about that person's system to troubleshoot. I should add that I had previously installed a lot of ported unix apps and libraries using Fink (see <http://fink.sourceforge.net>), and perhaps I have some things on my system needed for xgobi that a standard MacOS X/Darwin installation is missing. Dan -- Daniel E. Sabath, M.D., Ph.D. University of Washington Department of Laboratory Medicine Box 357110 Seattle, WA 98195-7110 USA Phone: (206) 598-6833 Fax: (206) 598-6189 http://www.labmed.washington.edu |
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From: <ja...@op...> - 2001-06-20 18:56:30
|
"Ron Ophir" <Ls...@wi...> writes:
> >>> Jason E. Stewart <ja...@op...> 06/20/01 05:18PM >>>
> "Ron Ophir" <Ls...@wi...> writes:
>
> > I am sending this mail directly to just because there is a problem
> > with the list-server.
>
> Hmmm. What problems?
>
> The error was very weird. somthing like the list was not found.
I'm not having any trouble, my replies to you are going through
fine. Let me know if you are still unable, and what the error message
is and I will fix it.
> > I run xml2db as followo: ./xml2db.pl
> > -f/usr/local/genex/submission/HopedulyMyFirst-298592356.10620/HopedulyMyFirst.xml
> > -Dgenex and got that error message: Using directory:
> > /usr/local/genex/submission/HopedulyMyFirst-298592356.10620/.
> > Reading GEML file: HopedulyMyFirst.xml...DONE. Can't call method
> > "getValue" on an undefined value at ./xml2db.pl line 1548.
>
> Seems that you have an external file section in the XML file, but that
> (at least) one of the external files has no 'id' attribute. Could you
> email me the 'HopedulyMyFirst.xml' file?
>
> I am sending you MySecond it gives the same error the name is
> shorter and with the stupid spelling error.
Here is the error:
<external_file_list>
<external_file
id="usf_file"
file_name="MySecond_USF_1.ext"/>
<external_file/>
^^^^^^^^^^^^^^^^
<external_file
id="alfile1"
file_name="MySecond_ALS_1.ext"/>
<external_file
id="alfile2"
file_name="MySecond_ALS_2.ext"/>
<external_file
id="amfile1"
file_name="MySecond_AMS_1.ext"/>
</external_file_list>
Notice the empty <external_file/>. The curation_tool has botched this
up somehow. When I delete this from the XML file it seems to progress
smoothly. Sorry to make you edit this by hand, but I don't know why
the CT generated a bogus file.
> I am sending you the JAR file.
> The control file includes the folowing lines:
[snip]
> I see the user ID but where should I put it as an argument.
Sorry Ron,
I'm not sure what you're asking here. Could you clarify?
jas.
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From: Harry M. <man...@ho...> - 2001-06-20 18:28:37
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Hi Qi, the XML::DOM is a standard module: Module XML::DOM (T/TJ/TJMATHER/libxml-enno-1.05.tar.gz) You might check to see if your CPAN sites are up to date or whether your firewall prevents you from installing via the cpan shell. or try to force it: perl -MCPAN -e 'install XML::DOM' or failing that, from within the CPAN shell, cpan> install T/TJ/TJMATHER/libxml-enno-1.05.tar.gz Cheers Harry Qi....@as... wrote: > > I was trying to download XML::DOM module before installing Genex. But I > could not find this perl module from CPAN. Could you please tell me where > to get it? Many Thanks > > Qi Zhang, Ph.D. -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Harry M. <man...@ho...> - 2001-06-20 18:17:37
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Hi Tony, John, Tony has looked at your data (and I should have immediately as well - sorry Tony) to find that it looks a bit suspect (see below) Tony Long wrote: > > Take the allgenes output and plot the mean expression level versus the standard > deviation (either Bayesian or actual) -- I attempted to put this below. > For some reason genes that are up regulated > have very low standard deviations and those down regulated very low. (sic) You mean 'very high', no? > We expect the standard deviation to be relatively constant with respect to > fold change. I suspect the last column (which again > I am guessing is average expression level -- since without that we can't > even do the analysis...) is calculated incorrectly OR there is some > strange experimental arrtefact we are not aware > of....Tony > > P.S. It would be helpful to spit back out the "average expression level" > for the paired analysis in the output file. You read my mind - I've been prepping a page that will do exactly that - a variety of descriptive stats in table form and graphics so people can get an idea of what their data looks like before they go forward, to be combined with some normalization that Michael Pear has been working on.. > > [Image] > > > attached as a gzipped file - unstuffit should handle this. > > > > Tony Long wrote: > > > > > > Harry: > > > > > > For some reason the data tried to be the text of the message > > > and failed to come through (w/o being screwed up). Can you save the > > > data as Word or Excel and make it an attachment, usually I have no > > > problem in that case. Tony > > > > > > > -- > > Cheers, > > Harry > > > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > > Content-Type: application/x-gzip; > > name="boyce-data.txt.gz" > > Content-Disposition: inline; > > filename="boyce-data.txt.gz" > > > > Attachment converted: Macintosh HD:boyce-data.txt.gz (????/----) (000473A0) > > -- > > Tony Long > > Ecology and Evolutionary Biology > Steinhaus Hall > University of California at Irvine > Irvine, CA > 92697-2525 > > Tel: (949) 824-2562 (office) > Tel: (949) 824-5994 (lab) > Fax: (949) 824-2181 > > email: td...@uc... > http://hjmuller.bio.uci.edu/~labhome/ -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: <ja...@op...> - 2001-06-20 14:18:35
|
"Ron Ophir" <Ls...@wi...> writes: > I am sending this mail directly to just because there is a problem > with the list-server. Hmmm. What problems? > I run xml2db as followo: ./xml2db.pl > -f/usr/local/genex/submission/HopedulyMyFirst-298592356.10620/HopedulyMyFirst.xml > -Dgenex and got that error message: Using directory: > /usr/local/genex/submission/HopedulyMyFirst-298592356.10620/. > Reading GEML file: HopedulyMyFirst.xml...DONE. Can't call method > "getValue" on an undefined value at ./xml2db.pl line 1548. Seems that you have an external file section in the XML file, but that (at least) one of the external files has no 'id' attribute. Could you email me the 'HopedulyMyFirst.xml' file? Thanks, jas. |
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From: Harry M. <man...@ho...> - 2001-06-19 23:28:15
|
John Boyce wrote: > > Hi Harry, > thanks for the reply. > I have attached the file for you to try. I used the Bonferroni > correction and that is column 4 in the file. Column 0 is the gene IDs > and columns 1, 2 and 3 are the logged data. When I set the Bonferroni > correction false positive rate to 0.01 I get significant genes and many > of these are biologically real (as this is just a test heat shock exp I > know many genes to expect). It only picks upregulated genes but I think > that there are a number of significant down regulated genes as well. There's obviously some kind of bug - it's probably sorting on the 't' value rather than the 'p' value (an off-by-one mistake). If you look at the ALLGENES gene list, you'll see that it's correctly sorted..... Yup - I think I've found the bug an it is an off-by-one column comparison. I've sent the patch to the author to make sure; as soon as he replies, I'll patch the running server. I should have noticed this before - it was also giving far too many significant genes as well as never marking any decreases as significant. We owe you several beers. Thanks! I'll email a note when I confirm it with Tony. > I still only get one graph even though it looks like you should get other > printouts if you have significant genes No, the pierre.pair function only has a single plot associated with it, so while it may not be as expected, it IS as programmed. However, if you want to examine all the variables to investigate the possible relationships, you can use xgobi to generate these plots, either by using it from the server (might be quite a bit of network latency to .au tho.) or by downloading the files generated and running it locally (but this requires local linux/unix machine, which I'm not sure you have.. > and the output as excel files > won't open on either my PC or Mac (I have tried using both servers). > When trying to open the excel files it says they may be read only or > there may be a network error. Also the data is from a two color > experiment so the columns of data are natural logs of the ratios of > cy3/cy5 for three separate measurements. I would be grateful if you > could have a look and see what you get. Infortunately (?), I still get valid Excel files on my end, whether generated on the Linux box and opened on a PC (file transfer by samba), or by doing everything on the PC. I also tried it on my Mac w/ Excel98 and it also opened. Maybe you could send me one of the suspect Excel files and I could see if there's something wrong with it..? You don't order your bytes upside down down under, do you? Can you find another PC or version of Excel to try? ALternatively since all the versions I have are later than '97, it may be a '97 bug..? > John -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Harry M. <man...@ho...> - 2001-06-19 16:07:12
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Nicolas Bertrand wrote: > > Hello > > Sorry for the lack of update on the installation of genex on our mac running macosx. I have been away. > > Looks like only one required package is missing before I can set up the server. The package is xgobi. Has anybody successfully installed xgobi in MacOSX? > > Log for the installation of xgobi: > > [localhost:Shared/xgobi/src] nicolasb% make > Makefile:1: *** missing separator. Stop. > [localhost:Shared/xgobi/src] nicolasb% ls make* > make_axes.c > [localhost:Shared/xgobi/src] nicolasb% ls *ake* > Makefile Makefile.example make_axes.c > [localhost:Shared/xgobi/src] nicolasb% mv M > Makefile Makefile.example > [localhost:Shared/xgobi/src] nicolasb% mv Makefile.example M > Makefile Makefile.example > [localhost:Shared/xgobi/src] nicolasb% mv Makefile.example Makefile > [localhost:Shared/xgobi/src] nicolasb% make It looks like you had some troubles with creating the makefile. Did you try to use xmkmf? ie: % cd /path/to/xgobi/src % xmkmf mv -f Makefile Makefile.bak imake -DUseInstalled -I/usr/X11R6/lib/X11/config (creates a Makefile that is specific for your system) [most lines deleted] > cc -g -o xgobi xgobi.o xgobi_init.o pipeline.o read_array.o initialize.o widgets.o callbacks.o getfname.o xyplot.o make_axes.o line_editor.o missing.o spin_cbacks.o spin.o scaling.o scale_cbacks.o identify.o var_panel.o transform.o exclusion.o inference.o DrawingA.o stdize.o brush_init.o brush_cbacks.o brush.o paint.o brush_send.o help.o prt_plotwin.o subset.o vc_lists.o plot_once.o plot1d.o ash1d.o texture.o move_points.o show_message.o smooth.o smooth_fns.o smoothsk.o pspline.o save_data.o new_data.o read_data.o jitter.o parcoords.o utils.o tour_init.o tour_util.o tour.o tour_cbacks.o tour_send.o gt_ctls.o tour_pp.o svd.o kernel.o legendre.o hermite.o natrl_hermite.o de_indices.o central_mass.o holes.o skewness.o tour_section.o corr.o corr_index.o corr_pursuit.o corr_util.o -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11 -lm > /usr/bin/ld: Undefined symbols: > _open_sphere_popup_cback > _genrand > _sgenrand > make[1]: *** [xgobi] Error 1 > make: *** [all] Error 2 these calls are not made in the xgobi code, so they have to be called in functions that xgobi calls. I've never heard of them. They sound like native xgobi calls but those strings are never used in the entire xgobi tree. Maybe David (Daniel E Sabath <dsabath@u.washington.edu>), who has gotten GeneX running on his OSX can comment? Harry -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Nicolas B. <nic...@pl...> - 2001-06-19 10:29:31
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Hello Sorry for the lack of update on the installation of genex on our mac running macosx. I have been away. Looks like only one required package is missing before I can set up the server. The package is xgobi. Has anybody successfully installed xgobi in MacOSX? Log for the installation of xgobi: [localhost:Shared/xgobi/src] nicolasb% make Makefile:1: *** missing separator. Stop. [localhost:Shared/xgobi/src] nicolasb% ls make* make_axes.c [localhost:Shared/xgobi/src] nicolasb% ls *ake* Makefile Makefile.example make_axes.c [localhost:Shared/xgobi/src] nicolasb% mv M Makefile Makefile.example [localhost:Shared/xgobi/src] nicolasb% mv Makefile.example M Makefile Makefile.example [localhost:Shared/xgobi/src] nicolasb% mv Makefile.example Makefile [localhost:Shared/xgobi/src] nicolasb% make make xgobi cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" xgobi.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" xgobi_init.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" pipeline.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" read_array.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" initialize.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" widgets.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" callbacks.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" getfname.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" xyplot.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" make_axes.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" line_editor.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" missing.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" spin_cbacks.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" spin.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" scaling.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" scale_cbacks.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" identify.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" var_panel.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" transform.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" exclusion.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" inference.c -I/usr/X11R6/include inference.c: In function `sort_cback': inference.c:234: warning: passing arg 4 of `qsort' from incompatible pointer type cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" DrawingA.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" stdize.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" brush_init.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" brush_cbacks.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" brush.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" paint.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" brush_send.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" help.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" prt_plotwin.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" subset.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" vc_lists.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" plot_once.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" plot1d.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" ash1d.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" texture.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" move_points.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" show_message.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" smooth.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" smooth_fns.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" smoothsk.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" pspline.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" save_data.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" new_data.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" read_data.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" jitter.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" parcoords.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" utils.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" tour_init.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" tour_util.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" tour.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" tour_cbacks.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" tour_send.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" gt_ctls.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" tour_pp.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" svd.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" kernel.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" legendre.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" hermite.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" natrl_hermite.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" de_indices.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" central_mass.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" holes.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" skewness.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" tour_section.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" corr.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" corr_index.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" corr_pursuit.c -I/usr/X11R6/include cc -g -c -DDEFAULTDIR=\"/Users/Shared/xgobi/src/..\" corr_util.c -I/usr/X11R6/include cc -g -o xgobi xgobi.o xgobi_init.o pipeline.o read_array.o initialize.o widgets.o callbacks.o getfname.o xyplot.o make_axes.o line_editor.o missing.o spin_cbacks.o spin.o scaling.o scale_cbacks.o identify.o var_panel.o transform.o exclusion.o inference.o DrawingA.o stdize.o brush_init.o brush_cbacks.o brush.o paint.o brush_send.o help.o prt_plotwin.o subset.o vc_lists.o plot_once.o plot1d.o ash1d.o texture.o move_points.o show_message.o smooth.o smooth_fns.o smoothsk.o pspline.o save_data.o new_data.o read_data.o jitter.o parcoords.o utils.o tour_init.o tour_util.o tour.o tour_cbacks.o tour_send.o gt_ctls.o tour_pp.o svd.o kernel.o legendre.o hermite.o natrl_hermite.o de_indices.o central_mass.o holes.o skewness.o tour_section.o corr.o corr_index.o corr_pursuit.o corr_util.o -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11 -lm /usr/bin/ld: Undefined symbols: _open_sphere_popup_cback _genrand _sgenrand make[1]: *** [xgobi] Error 1 make: *** [all] Error 2 -------------------------------------------------------------- Nicolas Bertrand Department of Plant Sciences University of Oxford Oxford OX1 3RB Tel: 01865 275 116 (Office) e-mail: nic...@pl... -------------------------------------------------------------- |
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From: Harry M. <man...@ho...> - 2001-06-18 18:50:49
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Hi John, Sorry for the delay in answering. John Boyce wrote: > > Hi Harry, > I am using http://genex.ncgr.org/cgi-bin/genex/cybert/CyberTDB-7.0.pl > site and have had a small number of problems. Firstly if I ask for the > gene list output in excel format I get a file, save it to my computer > and it looks like an excel file but as soon as I try to open it it > crashes excel (PC win 97 version). I've tried this on a variety of inputs and the Excel files I get back open correctly with Star Office, WingzPro and Excel2000 (running under vmware as well as running native). I don't have excel 97 on any machine - can anyone else verify that this is the case? I do see that there is one non-printable character at the end of some lines in Excel2000 (tho not in WingzPro), and Star Office does have to be explicitly formatted 'default' to see all the header lines. Alternatively, if the datase that you're using is very large, it might cause a problem; if it's not proprietary and you wouldn't mind shipping it to me, I can try to debug it locally. > Also I ask for the graphics to be > printed (2 per page or 1 per page) but get only a single graph out > entitled 'does difference predict significance'. Am I missing > something? Some graphics pages may be omitted if there isn't data to generate them - so if 'significant' genes aren't found, no gpaphics will be drawn for them. What analyses were you trying to do (C+E or Paired?) and what were the parameters you were using? And again, the data file would help to debug this... > However I am getting a nice gene list which agrees fairly well with what > I expect from my other analyses. Well, that's a relief, I guess ;). what other tools are you using and how do they compare with CyberT in terms of real utility for a biologist? I admit that the CyberT interface is pretty crude, but we're really trying for core utility and therefore very little user interface niceties have been implemented. > John > > Harry Mangalam wrote: > > > > Thanks for registering! Which loacation are you using it at? > > > > UCI [ http://genomics.biochem.uci.edu/genex/cybert ] > > gets the latest updates, but NCGR [ http://genex.ncgr.org/genex/cybert ] > > is updated only slightly later and runs on a much faster machine with more RAM. > > > > Please let us know what else you'd like to see it do.. > > > > Cheers > > Harry > > > > John Boyce wrote: > > > > > > Registering for cyberT > > > -- > > > > > > ********************************************************************* > > > John Boyce > > > Department of Microbiology > > > Monash University > > > 3800 > > > Australia > > > ph (w) +61 3 9905 4838 (h) +61 3 9376 6641 > > > mobile ph 0409 766642 > > > fax (w) +61 3 9905 4811 > > > ********************************************************************* > > > > -- > > Cheers, > > Harry > > > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > > -- > > ********************************************************************* > John Boyce > Department of Microbiology > Monash University > 3800 > Australia > ph (w) +61 3 9905 4838 (h) +61 3 9376 6641 > mobile ph 0409 766642 > fax (w) +61 3 9905 4811 > ********************************************************************* -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Harry M. <man...@ho...> - 2001-06-16 17:09:39
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7.0.3 should be fine. Harry qi zhang wrote: > > Hi, I would to try your Genex on my Suse Linux, which has Postgresql7.0.3 > installed. Do I have to upgrqade it to 7.1 or higher before installing > Genex? Can I stay with my current Postgresql? > > Thanks a lot. > > Regards. > > Qi Zhang, Ph.D. > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: <ja...@op...> - 2001-06-16 06:04:53
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Robin Cover, who manages one of the WWW's best XML/SGML sites has GeneXML. http://xml.coverpages.org/geneXML.html jas. |
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From: Harry M. <man...@ho...> - 2001-06-16 03:06:53
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Hi there,
It's complicated to keep all the requirements in one place and up to date and I think we have shorthanded part of the instructions asthe package that supplies this give not muc hindication that it
contains it. I'll change that info in the README.
In the README file it says:
In order to produce the html versions of the DTD's you will also
need a modified version of Earl Hood's excellent perlSGLML utilities
that we distribute from:
http://genex.ncgr.org/genex/download/genex-server/perlSGML.2001Jan23.tar.gz
but this makes no mention that it contains the dtd2html script that you need.
Mea culpa..
Install that package and it should cure at least that part of the installation
jj...@cs... wrote:
>
> Hi,
>
> in the What you need before you configure GeneX I could not find
> dtd2html, but the installation script requires this tool.
>
> Regards,
> Jochen Jaeger
--
Cheers,
Harry
Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
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From: <ja...@op...> - 2001-06-16 00:32:30
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"Jason E. Stewart" <ja...@op...> writes: > "Joe Roden" <ro...@ai...> writes: > > > > Can you reconfigure GeneX to *not* use tcp/ip to connect with the DB, > > > and give that a try. > > > > Will do, and that may well do the trick. That sounds like the sort of > > tweak that could cause the problem. > > Heh. > > Actually you *can't* configure genex to use tcp/ip sockets. No matter > what you tell it to use, the installation script forces communication > with a local Pg server :-( I know this must be the problem, because their was a typo in Genex.pm that prevented the use of a port number. So you must have been using Unix domain sockets to talk to the wrong DB all along. Ok. Fix is now checked into CVS. To get it do the following: $ cvs -d :pserver:ano...@ge...:/home/cvsroot/opengenex login (Logging in to ano...@ge...) CVS password: [no password, just hit enter] $ cvs -z3 -d :pserver:ano...@ge...:/home/cvsroot/opengenex \ co -r Rel-1_0_1-branch genex-server When you run install-all.pl, you will need to tell it that you are doing an update ([U] instead of [N]), and then tell it what the root of your previous installation was. Then go into prompting mode and specify the values for Host and Port that you *intended* to use all along. Let me know how it goes. jas. PS. If you don't want to get it from CVS for any reason, let me know and Harry or I will cut a new release this weekend. But be nice, I've got an OMG deadline on Monday, and a paper deadline the following Monday. So only ask *two* miracles from me ... ;-) |
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From: <ja...@op...> - 2001-06-15 23:59:26
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"Joe Roden" <ro...@ai...> writes:
> > Can you reconfigure GeneX to *not* use tcp/ip to connect with the DB,
> > and give that a try.
>
> Will do, and that may well do the trick. That sounds like the sort of
> tweak that could cause the problem.
Heh.
Actually you *can't* configure genex to use tcp/ip sockets. No matter
what you tell it to use, the installation script forces communication
with a local Pg server :-(
Ahem..
I took a look at the install-all.pl that you would be using (current
CVS version is 1.84, yours would have been 1.82) and the error is
still there. The problem is at around line 1671:
######################################################################
#
# GENEX_LOCAL -- set up final default connection parameters
#
######################################################################
if (defined $GENEX_LOCAL) {
$Vars{'GENEX_CONNECT'} = '$Bio::Genex::LOCAL = 1;';
$Vars{'GENEX_HOST'} = 'localhost';
$Vars{'GENEX_PORT'} = 5432;
$Vars{'GENEX_LOCAL'} = 1;
} else {
$Vars{'GENEX_CONNECT'} = '$Bio::Genex::HOST = \'' . $GENEX_HOST . "\';\n"
. '$Bio::Genex::PORT = ' . $GENEX_PORT . ";";
$Vars{'GENEX_HOST'} = $GENEX_HOST;
$Vars{'GENEX_PORT'} = $GENEX_PORT;
$Vars{'GENEX_LOCAL'} = 0;
}
The problem is $GENEX_LOCAL is *always* defined even if you tell it to
use tcp/ip sockets (it's set to '0') so the conditional is *always*
true.
Ouch.
Fix coming real soon to a strip-mall near you ...
jas.
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