EMBOSS: Project Meeting (Mon 11th June 07)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag
Apologies: Shaun McGlinchey, Martin Senger, Rodrigo Lopez, Tim Carver

1. Minutes of the last meeting

Minutes of the meeting of 14th May 2007 are here.

2. Software Development

2.1 Libraries

Peter has standardized function names in ajUtil and ajSys.

2.2 Windows

Alan is finishing the windows port which now includes gd to support png and other image formats.

David Judge visited last week to discuss EMBOSS interfaces for Windows local use. Tim has checked on the status of Jemboss on Windows. It is possible to build a cut-down version, which Alan can include in the Windows distribution bundlewin utility. This uses ant to build Jemboss, and produces a jar file. An installer will call a statically linked executable to create a jemboss.properties file.

Alan and Peter had a conference call with SciTegic last week. The latest EMBOSS windows has been bundled for testing. Currently the RTLs have to be downloaded, but SciTegic would like to include them in the distribution.

2.3 Other development

Alan is working on the conversion details for a contributed fragment assembly package. The ACD file has a very large number of options.

Peter updated phylipnew to read multiple distance matrices from a single input file, and has a test script for a number of phylip applications from a user in Canada.

We hope to migrate the old EMBOSS 2.8.0 SoapLab services to the new EMBOSS 4.1.0 services. To check whether this will affect any of the existing users, Mahmut has tested Taverna 1.5.2 workflows using the new EMBOSS 4.1 services. All examples worked. Mahmut will test command lines from other EMBOSS 2.8.0 soaplab service invocations.

Mahmut is monitoring a problem with "too many open files" in SoapLab. Most of the open files were pipes. He is also working on JAX-WS in SoapLab 2.

3. Administration

Alan is looking into specifications for a server, and into revised backup arrangements now all machines are in one location.

Alan will update the machines to Fedora 7 in the next 2 weeks.

3.1 Release 5.0.0

Peter will mail a request for users to nominate obsolete applications, and suggested replacements. Peter will mail a list of previously suggested new applications and feature requests from past email archives to complete the set on SourceForge.

4. Documentation and Training

4.1 Books

Jon reported that CUP would like to meet for a progress update.

Jon has updated the overall structure of all documents, working from the top level down. Each section has a short abstract for internal use as a guide to its purpose, and is checked with XMLMind although emacs is used for general editing. Jon will send out an updated contents list for each book and a list of the abstracts. About 60% of the section documents are now complete in draft form.

Recent additions are extended format descriptions for sequences, features and reports, and EMBOSS commandline usage. For developers the coding standards and code documentation standards have been tidied up.

After the release, we need to generate code test cases and examples for all major library functions.

4.2 Developer documentation

Following a request from Hamish McWilliam (EBI External services), Peter is looking at adding tables of contents for the library documentation, showing sections, subsections and functions at each level. This is relatively easy to add to the existing web pages, and Jon will be able to add the same feature to the new book pages.

Hamish has also asked for utilities (or an API) to report on the contents of index files. One use for this is to identify duplicate identifiers for the dbxflat indices. Alan will look into this for dbx indices. Peter will do the same for dbi indices.

5. User queries and answers

No new issues.

6. AOB


7. Date Of Next Meeting

The next meeting is on Monday 9th July.