[Bioperl-pipeline] Where is Bio::Annotation?

[Sang Chul Choi]

Dear biopipeline groups!

I have installed the biopipe as long as I could.

I followed the instruction at http://www.biopipe.org/bioperl-pipeline-run.html.

I run it. The result outputs are:

=============================================================================
Creating annotate_pipeline
   Loading Schema...
Reading Data_setup xml   : ../xml/templates/dev/genomic_sequence_annotation.xml
Doing DBAdaptor and IOHandler setup
Doing Transformers..
Doing Pipeline Flow Setup
Doing Analysis..
Doing Rules
Doing Job Setup...
Loading of pipeline annotate_pipeline completed
8 analysis found.
Running test and setup..

//////////// Analysis Test ////////////
Checking Analysis 1 DataMonger
-------------------- WARNING ---------------------
MSG: Skipping test for DataMonger
---------------------------------------------------
 ok
Checking Analysis 2 RepeatMaskerUpdating Program version to 07/07/2001
 ok
Checking Analysis 3 blast ok
Checking Analysis 4 blast ok
Checking Analysis 5 blast ok
Checking Analysis 6 blast ok
Checking Analysis 7 blast ok
Checking Analysis 8 blast ok
Fetching Jobs...
Fetched 1 incomplete jobs
Running job /tmp/annotate_pipeline_DataMonger.1046336389.115.out /tmp/annotate_pipeline_DataMonger.1046336389.115.err
Fetched 1 completed jobs
Going to snooze for 3 seconds...
Waking up and run again!
Fetching Jobs...
Fetched 2 incomplete jobs
Running job /tmp/annotate_pipeline_RepeatMasker.1046336390.570.out /tmp/annotate_pipeline_RepeatMasker.1046336390.570.err
=============================================================================

Then, I read the file, "/tmp/annotate_pipeline_RepeatMasker.1046336390.570.err". The file contains:

=============================================================================
READING: Lost the will to live Error. Problems with runnableDB fetching input
[
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::BioToEns::Beacon. Can't locate Bio/Annotation.pm in @INC (@INC contains: /usr/local/lib/perl5
/5.8.0/i686-linux /usr/local/lib/perl5/5.8.0 /usr/local/lib/perl5/site_perl/5.8.0/i686-linux /usr/local/lib/perl5/site_perl/5
.8.0 /usr/local/lib/perl5/site_perl .) at /usr/local/lib/perl5/site_perl/5.8.0/Bio/EnsEMBL/Virtual/StaticContig.pm line 54, <
STDIN> line 1.
=============================================================================

Bioperl complains of the lack of Bio/Annotation.pm. I cound not find it even bioperl-xxxxxx cvs repositary.

Thank you very much for reading my letter.

Sincerely yours,

Sang Chul Choi-------------- next part --------------
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