From ajt at rri.sari.ac.uk  Tue Jun  6 09:33:09 2006
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Tue, 06 Jun 2006 14:33:09 +0100
Subject: [Bio-Linux] Installing Bio-Linux packages under Ubuntu
Message-ID: <44858415.7040804@rri.sari.ac.uk>

Hello, Bio-Linux'ers

As part of my NuGO 'Black-Box' project, I've been comparing Ubuntu 
'Dapper' and Debian 'Etch': One reason why I hesitated to adopt Ubuntu 
'Dapper', initially, is that the Bio-Linux 'base-directories' package 
has a dependency on Debian 'xlibs' which is not present in Ubuntu 
'Dapper'. This package is, however, present in Ubuntu 'Hoary', so I 
installed the 'xlibs' package from 'Hoary' into 'Dapper' and Bio-Linux 
now installs and runs OK under Ubuntu (with the sun-java packages).

The 'xlibs' package is a transitional package, which has dependencies 
that help when installing X11, but it only contains documentation in 
Ubuntu 'hoary'. It is absent in 'Dapper' and is deprecated in 'Etch'.

Another question I have is that although it's possible to run 32-bit 
binaries in the 64-bit (amd64) version of 'Dapper' I can't install the 
Bio-Linux packages from the NEBC repository because "apt" wants to find 
amd64 binaries: Is there some apt magic I can use to force an amd64 
Ubuntu system to use the 32-bit packages for i386 in your repository?

So far, I've just downloaded the 32-bit debs manually onto the 64-bit 
system, and tried them out.

I think that Bio-Linux is a great project, and I've already found it 
very useful for my own work. However, I'd like to see it flourish in a 
more platform-independent way. I'd be interested to hear from anyone 
else using Bio-Linux packages on non-NEBC-Dell Bio-Linux machines. We're 
running it on a variety of different hardware including uniprocessor and 
SMP: i386, Athlon, Athlon64, Opteron and on several different software 
platforms including Red Hat 9, Debian 'Etch' and Ubuntu 'Dapper'.

Best wishes,

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687



From asmo at ceh.ac.uk  Tue Jun  6 09:38:20 2006
From: asmo at ceh.ac.uk (Ashley Morley)
Date: Tue, 06 Jun 2006 14:38:20 +0100
Subject: [Bio-Linux] Installing Bio-Linux packages under Ubuntu
	(Out of office reply)
Message-ID: <s4859384.020@wpo.nerc.ac.uk>

Hi, 
I am out of the office until 12th June. If urgent, please contact the NEBC at helpdesk at nebc.nox.ac.uk 

Kind regards
Ashley



From nathanhaigh at ukonline.co.uk  Fri Jun 16 03:29:16 2006
From: nathanhaigh at ukonline.co.uk (Nathan S. Haigh)
Date: Fri, 16 Jun 2006 08:29:16 +0100
Subject: [Bio-Linux] KEGG SOAP API
Message-ID: <000601c69116$92f55ee0$2d0d6d58@nathan243dd61f>

I'm trying to install Apache Axis libraries following the instructions at:

http://www.genome.jp/kegg/soap/doc/keggapi_manual.html#label:8

 

I copy the libraries to /usr/local/java/lib/

And then try the first command mentioned on this page:

java -classpath
/path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.j
ar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsd
l4j.jar:. org.apache.axis.wsdl.WSDL2Java -p keggapi
http://soap.genome.jp/KEGG.wsdl

 

I then get an error:

Exception in thread "main" java.lang.NoClassDefFoundError:
org.apache.commons.logging.LogFactory

        at
org.apache.axis.components.logger.LogFactory.class$(LogFactory.java:45)

        at
org.apache.axis.components.logger.LogFactory$1.run(LogFactory.java:45)

        at java.security.AccessController.doPrivileged(Native Method)

        at
org.apache.axis.components.logger.LogFactory.getLogFactory(LogFactory.java:4
1)

        at
org.apache.axis.components.logger.LogFactory.<clinit>(LogFactory.java:33)

        at
org.apache.axis.i18n.ProjectResourceBundle.<clinit>(ProjectResourceBundle.ja
va:53)

        at
org.apache.axis.i18n.MessagesConstants.<clinit>(MessagesConstants.java:32)

        at org.apache.axis.utils.Messages.<clinit>(Messages.java:36)

        at org.apache.axis.wsdl.WSDL2Java.<clinit>(WSDL2Java.java:112)

 

Has anyone tried this installation, or do you have any suggestions?

 

Thanks

Nathan

 

----------------------------------------------------------------------------
------

Dr. Nathan S. Haigh MPharmacol. Ph.D.

Bioinformatics PostDoctoral Research Associate

 

Room B2 211                                            Tel: +44 (0)114 22
20112

Department of Animal and Plant Sciences                Mob: +44 (0)7742 533
569

University of Sheffield                                Fax: +44 (0)114 22
20002

Western Bank                                           Web:
www.bioinf.shef.ac.uk <http://www.bioinf.shef.ac.uk/> 

Sheffield
www.petraea.shef.ac.uk

S10 2TN                                         

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------

 

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From ajt at rri.sari.ac.uk  Fri Jun 16 05:26:42 2006
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Fri, 16 Jun 2006 10:26:42 +0100
Subject: [Bio-Linux] KEGG SOAP API
In-Reply-To: <000601c69116$92f55ee0$2d0d6d58@nathan243dd61f>
References: <000601c69116$92f55ee0$2d0d6d58@nathan243dd61f>
Message-ID: <44927952.7010603@rri.sari.ac.uk>

Nathan S. Haigh wrote:
> I?m trying to install Apache Axis libraries following the instructions at:
> 
> http://www.genome.jp/kegg/soap/doc/keggapi_manual.html#label:8
> 
>  
> 
> I copy the libraries to /usr/local/java/lib/
> 
> And then try the first command mentioned on this page:
> 
> java -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.jar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsdl4j.jar:. org.apache.axis.wsdl.WSDL2Java -p keggapi http://soap.genome.jp/KEGG.wsdl
 > [...]

Hello, Nathan.

You have to use a "/path/to/lib" appropriate for your own system!

try:

java -classpath 
/usr/local/java/lib/axis.jar:/usr/local/java/lib/jaxrpc.jar:/usr/local/java/lib/commons-logging.jar:/usr/local/java/lib/commons-discovery.jar:/usr/local/java/lib/saaj.jar:/usr/local/java/lib/wsdl4j.jar:. 
org.apache.axis.wsdl.WSDL2Java -p keggapi http://soap.genome.jp/KEGG.wsdl

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687



From n.haigh at sheffield.ac.uk  Fri Jun 16 09:27:24 2006
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Fri, 16 Jun 2006 14:27:24 +0100
Subject: [Bio-Linux] KEGG SOAP API
In-Reply-To: <44927952.7010603@rri.sari.ac.uk>
Message-ID: <000c01c69148$9adc27b0$2d0d6d58@nathan243dd61f>

Sorry for the misunderstanding, I just copied and pasted the command from
the web site. I did in fact use /usr/local/java/lib/. Any other suggestions?

Thanks
Nathan

-----Original Message-----
From: bio-linux-bounces at envgen.nox.ac.uk
[mailto:bio-linux-bounces at envgen.nox.ac.uk] On Behalf Of Tony Travis
Sent: 16 June 2006 10:27
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] KEGG SOAP API

Nathan S. Haigh wrote:
> I'm trying to install Apache Axis libraries following the instructions at:
> 
> http://www.genome.jp/kegg/soap/doc/keggapi_manual.html#label:8
> 
>  
> 
> I copy the libraries to /usr/local/java/lib/
> 
> And then try the first command mentioned on this page:
> 
> java -classpath
/path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.j
ar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsd
l4j.jar:. org.apache.axis.wsdl.WSDL2Java -p keggapi
http://soap.genome.jp/KEGG.wsdl
 > [...]

Hello, Nathan.

You have to use a "/path/to/lib" appropriate for your own system!

try:

java -classpath 
/usr/local/java/lib/axis.jar:/usr/local/java/lib/jaxrpc.jar:/usr/local/java/
lib/commons-logging.jar:/usr/local/java/lib/commons-discovery.jar:/usr/local
/java/lib/saaj.jar:/usr/local/java/lib/wsdl4j.jar:. 
org.apache.axis.wsdl.WSDL2Java -p keggapi http://soap.genome.jp/KEGG.wsdl

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687

_______________________________________________
Bio-linux mailing list
Bio-linux at envgen.nox.ac.uk
http://envgen.nox.ac.uk/mailman/listinfo/bio-linux



From ajt at rri.sari.ac.uk  Fri Jun 16 11:46:36 2006
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Fri, 16 Jun 2006 16:46:36 +0100
Subject: [Bio-Linux] KEGG SOAP API
In-Reply-To: <000c01c69148$9adc27b0$2d0d6d58@nathan243dd61f>
References: <000c01c69148$9adc27b0$2d0d6d58@nathan243dd61f>
Message-ID: <4492D25C.4020607@rri.sari.ac.uk>

Nathan S. Haigh wrote:
> Sorry for the misunderstanding, I just copied and pasted the command from
> the web site. I did in fact use /usr/local/java/lib/. Any other suggestions?

Hello, Nathan.

Which version of Tomcat are you using?

We had similar problems deploying base2 with the Debian/Ubuntu version 
of Tomcat, and downloaded the latest platform-independent tarball instead:

http://www.mirror.ac.uk/mirror/ftp.apache.org/tomcat/tomcat-5/v5.5.17/bin/apache-tomcat-5.5.17.tar.gz

It seems that using the built-in Java 1.4 compiler on earlier versions 
of Tomcat can cause compatibility problems, and the suggested 
work-arounds for using Java 1.5 with Tomcat 5.0 didn't work for us :-(

Best wishes,

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687



From n.haigh at sheffield.ac.uk  Fri Jun 16 09:27:24 2006
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Fri, 16 Jun 2006 14:27:24 +0100
Subject: [Bio-Linux] KEGG SOAP API
In-Reply-To: <44927952.7010603@rri.sari.ac.uk>
Message-ID: <000c01c69148$9adc27b0$2d0d6d58@nathan243dd61f>

Sorry for the misunderstanding, I just copied and pasted the command from
the web site. I did in fact use /usr/local/java/lib/. Any other suggestions?

Thanks
Nathan

-----Original Message-----
From: bio-linux-bounces at envgen.nox.ac.uk
[mailto:bio-linux-bounces at envgen.nox.ac.uk] On Behalf Of Tony Travis
Sent: 16 June 2006 10:27
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] KEGG SOAP API

Nathan S. Haigh wrote:
> I'm trying to install Apache Axis libraries following the instructions at:
> 
> http://www.genome.jp/kegg/soap/doc/keggapi_manual.html#label:8
> 
>  
> 
> I copy the libraries to /usr/local/java/lib/
> 
> And then try the first command mentioned on this page:
> 
> java -classpath
/path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.j
ar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsd
l4j.jar:. org.apache.axis.wsdl.WSDL2Java -p keggapi
http://soap.genome.jp/KEGG.wsdl
 > [...]

Hello, Nathan.

You have to use a "/path/to/lib" appropriate for your own system!

try:

java -classpath 
/usr/local/java/lib/axis.jar:/usr/local/java/lib/jaxrpc.jar:/usr/local/java/
lib/commons-logging.jar:/usr/local/java/lib/commons-discovery.jar:/usr/local
/java/lib/saaj.jar:/usr/local/java/lib/wsdl4j.jar:. 
org.apache.axis.wsdl.WSDL2Java -p keggapi http://soap.genome.jp/KEGG.wsdl

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687

_______________________________________________
Bio-linux mailing list
Bio-linux at envgen.nox.ac.uk
http://envgen.nox.ac.uk/mailman/listinfo/bio-linux