These are now used to store the list of chromosomes for species as well as the index for MAF files.
MAF tools have been enhanced to make use of index files when available.
TODO: When datasets are purged from disk, these files should also be purged.
MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
With these notes:
User's can now specify the warnings that they which to report ('nowarns'). There are likely more options but they are unknown.
Using Firefox 1.5.0.12 on Ubuntu with no extensions/addons installed gives me no issues with loading the applet while Javascript is enabled or disabled (works for me).
TODO: Allow annotations to be specified for all species in the file, not just the
'primary' organism (as specified by the dbkey). Metadata for sequences will need to be
fleshed out more first (i.e. store all species present in the file).
Daniel Blankenberg