[Bioperl-pipeline] Annotation example error

[McWilliam, Sean (LI, Uni of Queensland)]

Hi again,

	Thanks for the new xml.
The pipeline database seems to be updated correctly now, I do have data in
the job table 
which wasn't the case previously.

Although the example documentation suggest altering PipeConf.pm after
running Xml2Db.pl,
I found I had to do this first as I wanted to alter the value for the tmp
directory, otherwise
the job table had /data0/tmp/ as the stdout, stderr etc directory (which I
dont have).

Running PerlManager.pl -l now gives errors about not being able to locate
perl modules

Can't locate Bio/Cluster/Family.pm in @INC (@INC contains:
/usr/local/ensembl/ensembl/modules /usr/local/ensembl/bioperl-live
/usr/local/ensembl/ensembl-external/modules
/usr/local/ensembl/ensembl-trace/modules /usr/local/ensembl/bioperl-db
/usr/local/ensembl/bioperl-pipeline /usr/local/ensembl/bioperl-run
/usr/local/ensembl/ensembl-pipeline/modules /usr/lib/perl5/5.6.1/i386-linux
/usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux
/usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl/5.6.0/i386-linux
/usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl .) at
/usr/local/ensembl/bioperl-run/Bio/Tools/Run/TribeMCL.pm line 153.
BEGIN failed--compilation aborted at
/usr/local/ensembl/bioperl-run/Bio/Tools/Run/TribeMCL.pm line 153.
Compilation failed in require at
/usr/local/ensembl/bioperl-pipeline/Bio/Pipeline/Runnable/TribeMCL.pm line
42.
BEGIN failed--compilation aborted at
/usr/local/ensembl/bioperl-pipeline/Bio/Pipeline/Runnable/TribeMCL.pm line
42.
Compilation failed in require at PipelineManager.pl line 26.
BEGIN failed--compilation aborted at PipelineManager.pl line 26.

I have downloaded the latest cvs releases for the required packages and
Bio/Cluster/Family.pm does not seem to exist.
There is a Bio/Cluster/FamilyI.pm in bioperl-live.
Also Bio/Seq/SeqBuilder.pm does not exist in the bioperl-live package
downloaded via command line cvs, but does exist
in the bioperl-live package downloaded as a tarball from the WebCVS site.
So how do I ensure I have the correct releases of all the required packages?

Cheers,
Sean



-----Original Message-----
From: shawnh@fugu-sg.org [mailto:shawnh@fugu-sg.org]
Sent: Tuesday, 22 October 2002 2:00 AM
To: McWilliam, Sean (LI, Uni of Queensland)
Cc: 'bioperl-pipeline@bioperl.org'
Subject: RE: [Bioperl-pipeline] Annotation example error


Hi Sean,
	I just found out what was the problem. The developer cvs
and the public cvs are somehow not in sync. THe version of the xml
which I committed doesn't seem to have found its way to the public cvs
repository.
weird. Will try and find out whats going on.
in the mean time, I have put the xml up on the web for download.

http://www.biopipe.org/download/genomic_sequence_annotation.xml

but it may not work if the code was not updated as well.

cheers,

shawn

********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************