[Bioperl-pipeline] Missing module in 0.1 tarball
Shawn Hoon
shawnh at fugu-sg.org
Wed May 7 09:54:04 EDT 2003
Hi Alistair,
>
> I'm now at the point of trying to populate a db using the Xml2DB.pl
> script. This doesn't work out of the box as it's complaining about a
> Converter module. In Xml2DB.pl:
>
> - Line 28: use Bio::Pipeline::Utils::Converter
> - Line 325: my $converter_obj = new Bio::Pipeline::Converter(
> - Line 373: my $converter_obj = Bio::Pipeline::Utils::Converter->new
>
> The error message on running the script is the old can't locate in INC
> blah, blah. If I comment out line 28 (and add an exit soon after)
> it's fine.
>
> There are two issues with this:
> - there is some inconsistency as to where the module actually is.
> - and I can't find the module in either of these locations above.
>
This is a deprecated script that has yet to be removed. I will do so
right now. The PipelineManager (not PipelineManager.pl -> also to be
removed)
is the script that lets you load and run pipelines:
To Load and not run :
> cd bioperl-pipeline/scripts:
> perl PipelineManager -dbname mydbname \
-dbuser <user> \
-dbhost <host> \
-xml
~/biopipe_release/xml/templates/examble/blast_biosql_pipeline.xml
-norun
To run:
> perl PipelineManager -dbname mydbname \
-dbuser <user> \
-dbhost <host> \
-queue priority
if you simple want to load and run just specify the first command above
without the -norun option.
This should be documented in the README that came with the bundle but
I'm sure the reference to XML2DB.pl is lying
somewhere on the website and needs correcting.
cheers,
shawn
> Best
>
> Alistair
>
> --
> Alistair G. Rust Senior Research Scientist
> Institute for Systems Biology 1441 North 34th St.
> arust AT systemsbiology.org
> Seattle, WA 98103 8904 http://www.systemsbiology.org
>
>
>
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>
More information about the bioperl-pipeline
mailing list