EMBOSS: Project Meeting (Dec 20th 1999)


Sanger Centre: Peter Rice, Ian Longden
HGMP: Alan Bleasby, Gary Williams, Val Curwen, SInead O'Leary

1. Matters Arising

2. General progress on release 0.0.4

The dbi indexing programs are now working.

Peter still needs to implement a "-batch" option.

The ACD documentation has been updated to include the latest data types, qualifiers and attributes.

HGMP would like to include a PISE interface to EMBOSS in their February training courses.

Val's tutorial should be added to the web pages. The original is in Latex.

-sprotein and -snucleic options have been added to force the sequence type. -sprompt is no longer in use (replaced by -sask to avoid a clash with -sprotein). No users have complained, so it is assumed that nobody was using this option (-sbegin and -send are generally easier).

Peter has started updating the application documentation. There are tables of command line options automatically built by "-help -acdtable". Author information is in an include file so any author can be automatically updated. Target users is also in an include file, but needs to be updated throughout. We still need examples for each application, and standard information on the sequence options.

HTML and plain text version of the documentation are still required. Peter wiull work on modifying a Sanger script to convert the web pages into a stand-alone distributable form.

For PHYLIP, ACD will need to accept a list of integer or float values, with some validation (min, max, total).

PHYLIP and MSE now build their own separate distributions.

Installation of PHYLIP and MSE needed changes to ACD file detection so that these packages can find their own ACD files, usually under a /usr/local/share/package directory. This will be documented in each package's INSTALL file.

The extra packages should be under an EMBASSY directory on the FTP server.

3. Any Other Business

The Dec 17th CCP11 workshop on open source software was very useful.

There is a need for an XML sequence format. EMBOSS could set a trend by using the readseq version.

Thje Xmas kitty is closed. All bug fixes are now free, at leat for the rest of the year.

4. Next meeting

Next meeting, after the holidays, will be Monday 10th January 2000, 11:00am, usual place.