EMBOSS: Project Meeting (Mon 21st August 2006)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag, Shaun McGlinchey
Apologies: Rodrigo Lopez, Lisa Mullan

1. Minutes of the last meeting

Minutes of the meeting of 7th August 2006 are here.

2. Software Development

2.1 XML and DOM Library

Alan is working through Hugh's old ajgraphxml code and the use of X3D structures. The x3dedit utility shows a few minor errors in the use of extra nodes. The code will be converted to use the new ajdom library.

2.2 Release 4.0.0

Peter has been working on a fix for another reported bug in reverse strand nucleotide features. When features are reported in EMBL format the complement locations are incorrect. This led to the discovery that the report generating programs were failing to correctly store reverse orientation features. They should have start greater than length, and a strand of '-'. most programs were setting start < length and setting the strand explicitly. This is changed to call ajFeatNewII and ajFeatNewIIRev, and to make sure these functions check the orientation of start and end positions. The fix will include changes to a number of main programs. They will be put on the FTP server as a combination of several earlier feature/report fixes to avoid confusing or conflicting file updates.

Alan rebuilt the EMBASSY package distributions with a fix for SGI 32 and 64bit platforms.

2.3 Other development

Alan raised the question of version numbers for EMBASSY packages after several users reported problems caused by updating to EMBOSS 4.0.0 without installing EMBASSY distributions from the EMBOSS4.0.0 directory.

The conclusion was that combining EMBOSS and EMBASSY version numbers is not easy using the configure.in mechanism so we will continue the current advice to reinstall all EMBASSY packages, and keep monitoring the situation.

Shaun has a JAX-WS service running water using his local installation, and will now reimplement using the EMBOSS installation on the EBI web nodes.

Mahmut has found a memory leak in the SoapLab server failing to delete log class instances. Currently he is testing a 64bit EMBOSS and EMBASSY installation in a temporary location. There may be some issues in moving to a final install directory.

Peter and Mahmut will work on an eclipse environment for EMBOSS development and profiling.

Jon reported that Mike's algorithm is now working for multiple structures as input.

3. Administration

3.1 Purify

Alan is looking into purify licensing under the IBM PartnerWorld program.

3.2 Test systems

Alan reported that our HP contact appears to have left. He will try to track down a new contact to upgrade the two loan systems.

4. Documentation and Training

4.1 Website

Peter has added "page not found" pages to the website. There is a general page, and one specific to applications. It is possible to redirect individual pages using the .htaccess file. The current page will be left in place for now to try to catch sites still using the old URLs.

Hamish McWilliam at EBI has made a number of suggestions to improve the application documentation (more documentation and usage examples for all commandline qualifiers) and an update to the supported systems list. Peter and Alan will review these.

4.2 Books

Jon will work on the chapter outlines and shared content for the three CUP books.

Jon suggested DocBook is still the best way to make content available in book, HTML and PDF form, but it must be a very simple layout to allow stylesheet control.

4.3 Training

Peter and Jon will contact possible sponsors for an autumn developers course outside Hinxton.

Jon had a meeting on the possibility of reviving the CCP11 user training courses.

5. User queries and answers

The list was reviewed. Everyone should review the current list at sf.net/projects/emboss/ and close those already dealt with.

All new issues were considered to be resolved.

6. AOB

6.1 RPMs

Ryan Golhar has supplied RPMs for RedHat Enterprise Linux. These will be put on the FTP server in a contrib directory with a README explaining they are an external contribution.

7. Date Of Next Meeting

The next meeting is on Monday 4th September, although Peter may be away at a conference.