EMBOSS: Project Meeting (Fri 22nd July 2005)


RFCGR/HGMP: Alan Bleasby, Jon Ison, Gary Williams,
Sanger: Tim Carver
EBI: Peter Rice, Lisa Mullan


1. Minutes of the last meeting

Minutes of the meeting of 8th July 2005 are here

2. Software Development

2.1 Release 3.0.0

Alan described a few last-minute updates to the release, which was made as planned (as usual) on 15th July.

The new "dbx" indexing programs are being tested by at least one user. EBI will also test them for production use.

A minor case-sensitive issue with resource definitions for the new dbx indexing was corrected, and database names were set to a minimum of 2 characters to be consistent with USA requirements (a 1-character database name can look like a windows drive letter in a filename) and to match the pattern defined for database names in the ACD file.

PHYLIPNEW was released under the name "PHYLIP" as this was the name used in the configure file. The old PHYLIP 3.5 programs are declared obsolete and not included in the release. Users who request them can be given the latest 3.0.0 versions of the old EMBASSY package.

PHYLIPNEW caused some compiler warnings when distributions were tested - fixed and the distribution rebuilt. One was that "lobyte" is a macro under Solaris. Note that this is the name used in the original phylip code.

Peter will update to phylip 3.63 (or a later version if it appears in time).

The admin guide needs to be updated to 3.0.0. Alan noted that EMBASSY packages can be tricky to build because of dependencies on the locations of dependency files, etc when built from the distributions.

2.2 String Arrays

Jon has added functions for string array processing. Peter will review the code and compare to other places where string arrays are used (for example arrays built from lists of strings) to find a consistent usage pattern.

3. Administration

3.1 Release 3.0.0

Alan reported this was completed.

3.2 FTP server

Alan reported the new release is available from open-bio.org.

3.3 Mailing Lists

Alan reported the lists have been moved to emboss.open-bio.org

3.4 Bug tracking

Alan raised the need for a better bug tracking system. Currently we use sourceforge, with bug reports added by hand. We need to investigate bugzilla and similar systems.

4. Documentation & Training

4.1 Sourceforge website

Peter updated the website for the new release, and added the new Changelog file.

The FAQ list should be added somewhere.

4.2 Developer Training Courses

These should be revived following the move to EBI. The course is in need of updating, to include the myemboss package and new 3.0.0 features.

A new course later this year, and 4 more next year was suggested. The previous costs per delegate should be enough to cover costs.

A possibility of basic and advanced developers' courses was discussed. The current course is designed to be suitable for novice programmers.

4.3 Books

The book text should be started during the summer, after the move to EBI is completed.

4.4 Rocplot paper

Jon announced the rocplot paper has been accepted and is due out at the end of 2005.

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. AOB

7. Date Of Next Meeting

Next meeting will be the first since the relocation to EBI, Date/time to be announced later.