EMBOSS: Project Meeting (Mon 12th June 2006)

Attendees

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

1. Minutes of the last meeting

Minutes of the meeting of 31st May 2006 are here.

2. Software Development

2.1 Windows

Alan has built a windows version with an installer, bundled in one executable file. The user accepts the GPL licence. The installation path defaults to c:\emboss the only outstanding known issue is whether spaces in file paths would work.

Peter has successfully installed EMBOSSWIN. An extra line at the end of entret output turned out to be a standard newline in the Windows comand prompt window.

Alan has added a new CVS tree emboss-ms to hold "projects" for building plplot, clustalw, primer3, and others for EMBOSSWIN. So far plplot does not include libpng.

2.2 Other development

Alan is resuming work on the DOM parser library.

Peter is working on Henrikki Almusa's submissions. Digest is updated to work on multiple sequences. A program to generate random sequences (makeseq) is split into nucleotide (makenucseq) and protein (makeproseq) versions to make the ACD interfaces simpler. Pattern list files are to be tried this week. Peter will be in Helsinki later this week and will meet Henrikki. More news at the next EMBOSS meeting.

GFF3 is now used as the internal format for storing nucleotide feature annotation. Some of the changes also allowed the table of swissprot/pir feature key conversions to be removed. Each EFeatures file now has an internal identifier used to share annotation.

Jon has completed meme and mast, which only need to be committed and have QA tests defined.

3. Administration

3.1 Emboss-Submit Backlog

Peter will be discussing Henrikki's submissions with him and with Medicel in Helsinki later this week.

3.2 Release 4.0.0

Jon has reviewed the lists on emboss.sf.net and assigned priorities to them, based on ease of implementation, past commitments, and general importance. Those rated 6-9 should be in the release, 1-4 are non urgent.

4. Documentation & Training

4.1 Website updates

Peter will generate program and source docuemntation for past releases and copy to the website. The program documentation will be the standard release HTML files with only graphics to be included.

5. User queries and answers

The list was reviewed. Most had already been resolved.

6. AOB

7. Date Of Next Meeting

Next meeting is on a Tuesday again, 27th June. Back to the normal Mondays after that.