EMBOSS: Project Meeting (Mon 12th April 10)


EBI: Peter Rice, Alan Bleasby, Mahmut Uludag
Apologies: Jon Ison

1. Minutes of the last meeting

Minutes of the meeting of 29th March 2010 are here.

2. Maintenance etc.

2.1 Applications

Peter will look into a user request for polydot to display matching in both orientations as lines in opposite directions. It is not clear whether this should be on by default as short matches may appear as points.

Alan raised the issue of changes in MIRA 3.0 where options change according to the specified sequencing technology. Applications can be created for single technologies, but it is more complicated to cover cases of mixed input data. Peter will check through and consider the ACD implications.

New patches of EMBASSY packages are needed where the documentation fails to build, a problem reported for MIRA. Peter will check through the builds to identify any others.

Mahmut will try the word matching performance improvements (using Rabin-Karp) on supermatcher.

2.2 Libraries

Alan has added Microsoft versions for the new ajsys.c functions that replace bare system calls. This required an alternative structure for the AjPFile object as the Unix pid does not exist on Windows, and the Microsoft handles do not exist on Unix. The embossdatadoc script will need extending to allow this kind of ifdef and to document the pid and handles as being system -specific. This is not urgent as the Unix documentation is correct as is.

Alan pointed out that there are duplicate string (suffix S) and char* (suffix C) functions. Peter will check and make the string function call the char* version so we have one copy of each function. The string version was written first and should have been converted rather than duplicated.

A few system calls remain, for example in ajfile.c where there are dependencies on global variables for data files and a waitpid call on closing a pipe file. In ajseqdb.c there are signals and timeouts for Microsoft where the signal is set in one function and released in another.

Alan has added a new version of ajFileNewInPipe for Microsoft systems.

Alan will check on home directory functions on Microsoft systems to provide the equivalent of parsing ~username on Unix.

Peter will look into scalable graphics options. A user has requested PDF output. SVG is another possibility which plplot may support. There was a second user request for scalable PNG files which may be possible now that the graphics scaling code has been cleaned up. The default size PNG files have too few pixels for fine detail. A general graphics options could provide a scale factor for fixed-size graphics outputs. The graphics output format definitions could include a flag to determine whether this option applies to a particular output device.

2.3 SoapLab

Client libraries using gsoap and axis1 have been tested. Mahmut reported on tests by External Services when defining an extra type in the SoapLab typed interface. In C++ clients the behaviour of gsoap causes problems where the minoccurs and maxoccurs XSD attributes are defined but have their default value of "1".

2.4 Other

Mahmut discussed problems with the icon size generated for Jemboss by java webstart, The rectangular icon is reduced to an unrecognizable 32 by 32 square. Tim will be consulted on adding a new 32 by 32 icon for webstart. The current icon will be retained for web pages and other uses. Peter has looked at Galaxy definitions for EMBOSS applications, It seems to be simple to generate. He will try building an automatic version for the CVS code and comparing to the EMBOSS 5.0.0 definitions in the Galaxy distribution.

3. New developments

3.1 BioMart access

Alan is waiting for stub code to include BioMart as a database access method. Peter will add BioMart as a query and entry method using the example code from martquery.

3.1 DAS access

Peter attended the DAS workshop last week on campus. The new DAS 1.6 specification is not yet finalized. We can look into support for DAS 1.53 as well, in case DAS servers are slow to move to the new standard. DAS 1.6 included a query for the version number of the server so we can identify 1.6 and assume earlier versions are 1.53.

Mahmut has looked briefly into the coding requirements for a C DAS client. There were no other developers at the workshop with any code to offer.

3.2 EDAM

Mahmut reported that the BioCatalogue team inquired about possible support for SAWSDL annotations using EDAM. We can make SAWSDL-annotated SoapLab services under new URLs for testing. The CVS ACD files have been parsed to test extraction of annotation for SAWSDL.

4. Administration

Alan will remind the systems group that we are still waiting for a test server configuration.

5. Documentation and Training

5.1 Books

Jon is away this week.

Peter plans to test all URLs in the book text and report any that are not yet available. We can populate these before publication.

5.2 Documentation

Peter has updated the embossdoc and embossdatadoc scripts to enforce 4 spaces between functions, and added a script to reset to 4 lines between functions and purge any trailing white space in the source code.

Peter has started on generating XML documentation for library source code. This can be completed when Jon is back.

5.3 Training

Alan reported on a request from Dave Judge who had issues with a web proxy that required a password. He found a workaround this time. We should implement passwords in the proxy handling. Alan will set up an internal proxy for testing.

Mahmut has been invited to teach on a course in Turkey in the summer. No further details as yet.

6. User queries and answers

All outstanding queries put on the Sourceforge tracker.

7. AOB


8. Date Of Next Meeting

The next meeting will be on Monday 19th April.