[Bioperl-l] Bio::Tools::Run::WrapperBase: Capture the command thatis executed?

Chris Fields cjfields at illinois.edu
Mon Apr 19 10:30:04 EDT 2010

On Apr 19, 2010, at 9:09 AM, Peter wrote:

> On Mon, Apr 19, 2010 at 2:03 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
>> Hey Ben,
>> Yes, the new stuff is in the bioperl-dev/trunk
>> svn://code.open-bio.org/bioperl/bioperl-dev/trunk/Bio/Tools/Run
>> (code.open-bio.org was working as of this morning...)
>> This is all pretty experimental, so use at own risk. The XML-based
>> config system is experimental too at the moment (tho' all code
>> is available, in bioperl-dev/trunk/Bio/Tools). I've been getting
>> good feedback from other Bio* peeps, who are advocating using an
>> existing config standard like emboss ACD or the Galaxy format.
> The EMBOSS ACD format is text based and as such rather niche.
> I was more suggesting the ability to parse the EMBOSS ACD files
> into the chosen XML format would be a neat way to automatically
> generate wrappers for all the EMBOSS tools at once.
> The Galaxy workflow command line tool description is XML and,
> might be suitably general. There are likely others out there too
> (no sense reinventing the wheel if possible).


The discussion we've been having with SoC on this (I think Brad Chapman's comments in particular) make me think this isn't a completely resolved issue, possibly b/c deriving a generic system is either extremely hard, not interesting, or simply that no one has thought of it yet.  Galaxy XML is the closest I can think of to a standard that might work.  I agree completely re: comments on ACD.


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