EMBOSS: Project Meeting (Mon 13th October 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 29th September 2008 are here.

2. Software Development

2.1 Applications

Alan has completed the index deletion code for both kinds of tree. Any remaining bugs are expected to be only in the node balancing code.

Peter is running a full test of the profiled dbx code. The test run completed, but hit an error when closing the huge descriptions index. It is not clear whether this was a code or a disk problem. We will order a large local disk to repeat the test.

Peter has added a new application dbxreport to analyse the dbx index files and report total keys and free space. The output indicates possible index problems where the key numbers fail to add up. To support dbxreport, a new page type NumBucket was needed. The index reading code tests for both NumBucket and Bucket page type to provide back compatibility, but dbxreport will give incorrect results on index files with Bucket page type used for NumBucket pages.

Peter has fixed a problem in einverted which expected all ambiguity codes to be 'N'.

2.2 Libraries

Peter will add an attribute to integers in ACD to allow them to be returned as longs for large values.

2.3 SoapLab

Mahmut reported that LSF is now enabled on the SoapLab servers and is running very well.

Creating jobs but not starting the job caused some issues in the removal of old jobs.

Problems for a frequent user creating jobs through a python client have been resolved. This was related to SoapLab2 exceptions. These did not obey JavaBean rules and so cannot be used by Axis. They were replaced by the SoapLab 1.0 exception class.

The EBI wrapper services (WsBlast, etc.) are not included in SoapLab 2.0. These services can now be run from their own native web service interfaces.

Log message density has been reduced.

MIRA services are currently disabled. Work is needed to pass the directory and return filename. The output definition depends on the options. Input files have a prefix in the commandline. Some fixes to the ACD file and C source are needed. QA tests are complicated by the need to copy files and create a directory.

Job directories need to be restructured to reduce their size, possibly once per hour.

3. Administration

4. Documentation and Training

4.1 Books

Jon has text for the user guide available to send to CUP.

Comments on the admin guide are completed.

Further comments are added to the "to do" and remarks sections.

The chapters in the developer's guide have been rearranged. Jon will work on the text next month.

Book content needs to be put on the website to test the stylesheets.

4.2 Website

Alan is waiting for a reply from OpenBio about moving the EMBOSS website and starting a Wiki.

4.3 Publications

5. User queries and answers

No new issues.

6. AOB

A large local disk for emboss6 will be ordered.

The Fuse update is done. Mahmut noted that eclipse metadata has grown to 1GB so this is now not copied. Netbeans use has been reduced.

7. Date Of Next Meeting

Peter is on honeymoon for the next 2 weeks. The next meeting is on Monday 10th November