[EMBOSS] workflows/emboss

[a.garcia at imb.uq.edu.au]

We would like to present G-PIPE; is a tool for building 
work flows. It wraps analysis methods available in EMBOSS 
(all of them). G-PIPE is built on top of PISE; including 
new analysis methods is possible. Once the user defines 
the work flow he/she can monitor its execution. It is 
possible to dispatch jobs over different servers. The work 
flows once defined are stored as an XML file that can 
later be loaded and replicated. G-PIPE is now installed in 
a better server, we have tested it running some analysis 
work flows, so far so good. 
 http://130.102.113.135/gpipe.htm

In order to access GPIPE JAVA must be enabled; the user is 
presented with two frames, one on which a menu with 
different methods is presented, and another frame where 
the corresponding GUI for the selected analysis method is 
displayed. The user selects the first analysis method, 
decides which is the next step in the work flow, selects 
this next step and so on. A more detailed (not as much as 
we would like to offer) description of the process to 
build and share a work flow is available together with an 
example of a work flow at http://130.102.113.135/gpipe.htm 
the tool is available at 
 http://kun.homelinux.com/Pise/5.a/gpipe.html

Gpipe exports the workflows as XML files and also as perl 
scripts. If the user wants it is possible to load, run 
 and modify the scripts using a command line interface. 
G-PIPE uses BioPerl.  We advise those who are interested 
to read the few documentation available and run the 
example we provide. Thanks in advance.