EMBOSS: Project Meeting (Mon 10th July 2006)
1. Minutes of the last meeting
Minutes of the meeting of 27th June 2006 are
2. Software Development
2.1 DOM Library
Alan has completed work on the DOM library. The ajdom
code will be in the release as an alpha version, but not used in any
applications at this stage. First use will be for graphics output.
The library has generic entity references but has AJAX function names
(so there is no clash with the native library) and in that sense is
not fully compliant to the DOM standard. Some of the function
names are very long.
We will need a further library to read and validate the XML (and
should get XMLspy too). Alan is looking for a free library,
possibly xpat, but we may need to write our own eventually.
2.2 Final developments for Release 4.0.0
Alan has updated the sourceforge requests list to include the
recent addition of a ragging option to digest.
Mike's code is done. Cleaning up will wait until after the
- Replaced references to obsolete application names in
the ajdmx.c source file.
- Added a sort routine to directory list processing so the
domainatrix family of programs will produce consistent output file
ordering and naming across all platforms. This will avoid some
issues with QA testing consistency.
Updated HMMERNEW qualifier names to avoid possible clashes,
including renaming the "-n" option.
Mdified fuzztran, fuzzpro and fuzztran to always produce an
output report (suggested by Henrikki Almusa).
- Modified coderet to produce 3 separate output files, two for
nucleotide (mRNA and CDS) and one for the protein translations. This
allows us to set the sequence type for each file, and avoids mixing
protein and nucleotide sequences in a single file.
- Modified infoseq to provide more control over output delimiter,
and cleaned up some repetitive code.
- Modified einverted to produce a file with the sequences of
inverted repeats. The sequence name includes the
start/end position in the original sequence.
- Converted the output of prophet to align output type, and fixed a
minor documentation error.
- Updated the EFUNCREL and EDATAREL databases for the 4.0.0
release. The new version will appear when the EBI SRS server next updates.
- Completed QA tests for all EMBASSY applications apart from Vienna
where examples are not so easy to find - but there are some data fiels
in Ivo's thesis and others in various publications.
All other tests passed in the latest run.
- Renamed the old meme application (not to be released this time, but still
in the QA tests). It has been renamed omeme (it clashed with the ememe
wrapper!). The ememe QA test is using the latest native meme
version. Jon will add a test for an EMBOSS_MEME variable so we
can explicitly test each version to catch changes.
- Modified default prompts to include the knowntype string.
- Extended help output for all programs to include default
values and knowntypes for all data types, as in the acdtable output.
- Removed the now redundant acdtable section from the text
documentation. In previous releases it was included but never well
formatted. Both versions are retained in the HTML documentation for now.
Peter will update the website documentation later today.
Renamed emboss-ms. A copy has been given to SciTegic for testing.
3.1 Release 4.0.0
The final changes for the release have to be completed by Wednesday 12th so
Alan can package everything in good time for Saturday's release.
Backup disks are installed to copy data from all the emboss
machines. Peter has already found them invaluable.
4. Documentation and Training
Jon has had futher contact from Bela.
5. User queries and answers
The list was reviewed. All high priority issues are done in time for
the release. Everything else will wait.
7. Date Of Next Meeting
Peter is away in 2 weeks time, and we can have a break after the
release. The next meeting is on Monday 7th August.