This directory contains contributions of packages with Soaplab services. Actually, not services themselves (such as analysis tools) but metadata and other data that are needed to wrap the tools as Soaplab-based Web Services. Particularly for Gowlab-based services, it contains everything you need to have to provide such services from your side.

These packages are (well, should be) location independent and small (because they do not include Soaplab core classes). If you have a Soaplab binary distribution installed, you can just use the provided script ws/add-services that takes this package and merge it into existing installation. Details are in the Binary distribution Guide.

If you wish to pack your own set use Soaplab CVS task dist-services.

Here is a list of prominent set of services that are always available:

Soaplab services

EMBOSS services

Obviously you need to have EMBOSS installed first. Its installation is quite straightforward, more tricky part is to set up all the databases (actually, to have them).

The Soaplab service set for EMBOSS programs - because it contains all pre-generated metadata descriptions for all EMBOSS analysis tools - is bound to a particular EMBOSS release. The currently supported EMBOSS release is 2.8.0.

What happened if you try to use a newer EMBOSS release? You will be able to access only programs whose metadata are present - so no new programs. And you will be able to access only those features of those programs that have not changed their command-line appearance (in other words: they need to have the same structure and contents of their command lines). Otherwise, it may work.

During adding this service set you will be prompted to specify location where your EMBOSS is installed. You will be offered a default location /usr/local/emboss or - if exists - contents of the EMBOSS_HOME environment variable.

Soaplab services

InterProScan services

These Gowlab-based services allow access to the EBI's InterProScan services.

They are two versions of them. Historically the first one uses traditional Gowlab approach to screen-scrape InterProScan web pages. Its use is now obsolete and may disappear later (the name of this package contains via_webpages). But it may still be a good example for developers how to write their own Java plug-in for more sophisticated Gowlab services.

The other one uses internally yet another Web service (written by those close to the authors of the InterProScan web pages so any potential changes there will be reflected here). There is nothing special for the end users about this services - but again for plug-in developers it may be interesting to see how it uses Gowlab approach to call another Web service.

Soaplab services

Fasta services

These Gowlab-based services allow access to the EBI's Fasta services.

The Gowlab uses internally yet another Web Service (again written by the external services development team at EBI, notably by Sharmila Pillai). And, again, there is nothing special for the end users about this services: They still have the usual Soaplab API as any other Soaplab services (so they can be immediately seen and used by all Soaplab clients, such as Taverna). The plug-in developers may check the class fasta.ebi.NativeWSPlugin that connects Gowlab service to the Sharmila's Web service.

Soaplab services

WU-Blast services

These Gowlab-based services allow access to some of the EBI's WU-Blast services.

Again the Gowlab uses here internally yet another Web Service (again written by Sharmila Pillai). The plug-in developers may check the class wublast.ebi.NativeWSPlugin that connects Gowlab service to the Sharmila's Web service.