Pierre LINDENBAUM wrote: > Hi all, > I'm trying to use taverna, but I'm a little bit lost in the workbench about > how to find the right tool. For example, one common task I'd like to perform > would be:
One good place to start for common tasks is to look in the Local Java Widgets (in 1.7.1) or Localworker (in 2.0). The best documentation is probably that for 2.0 see http://www.taverna.org.uk/taverna-2-0/taverna-2-0-documentation/taverna-2-0-help/overview/design-perspective/activity-palette/local-worker-activity-definition/ (apologies for the long URL) There are also lots of examples in the pack on myExperiment: http://www.myexperiment.org/packs/32 > + open a tab delimited file To open a file use the "Read Text File" local worker. > + 'grep' for the SNPs ( lines containing the regex rs[0-9]+ ) I'd then feed the text file into a "Split string into string list by regular expression" with newline as the regular expression > + 'cut' the 'Xth' column containing the SNPs Then you can feed the result of that into "Filter list of strings extracting match to a regex" to get the Xth column of the lines > + find the positions of those SNP on a given build of the human genome ( > using the mysql anonymous server of the UCSC) > + find the distinct Genes overlaping those SNP ( again, using the mysql > anonymous server of the UCSC) I don't know, sorry. > + output the result to a file Use the "Write text file" local worker. > Can anyone help ? I would be interested in how you find the right nodes and > how you fill the information. The local workers can be very useful. To find other services, you can use a service registry like SeekDA at http://www.seekda.com , the EMBRACE registry at http://www.embraceregistry.net/ or the soon-to-arrive http://www.biocatalogue.org If you are using Taverna 1.7.1 then you can search for services in the Feta registry once you have downloaded the Feta plugin. Select under Tools -> Plugin manager. Click "Find new updates" and you should see the Feta plugin. Tick it and install. You may need to restart Taverna. After that you can find services by Clicking the "Discover" tab. It takes some time to start up initially. > Thanks in advance > > Pierre Alan ------------------------------------------------------------------------------ _______________________________________________ taverna-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/taverna-users Documentation: http://www.mygrid.org.uk/usermanual1.7/ FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq Biological Services: http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
