News/New WebApollo Release (2013/11/22)
There is a new release of WebApollo
available from the
WebApollo release website. The
updated server setup instructions are available on the WebApollo
Installation
page, and the WebApollo user guide has been
updated accordingly.
If you currently have WebApollo instances up, please make sure to read
the updated server setup instructions as some of the configuration files
have changed. Since we now support multiple annotation types, you might
want to upgrade your existing data stores to change transcripts to mRNAs
(the only supported transcript type in previous versions). See the
instructions on upgrading your data
store.
You can try the public demo at
http://genomearchitect.org/WebApolloDemo.
Summary of changes:
- using JBrowse 1.10.9 release
- new hybrid store (memory/disk) should use much less memory than the
pure memory store (with a small degrade in performance) - useful for
genomes with many annotations (you can configure which one to use as
best fits your needs)
- viewing of annotation info editor for users without write privilege
(cannot modify the data)
- FASTA data adapter
- different annotation info editor configurations for different
annotation types
- database/history merger tool (command line)
- data adapters now use iterators when exporting data (improves memory
footprint)
- add a configurable option for dumping owner and other meta-data to the
GFF3 adapter
- undoing an “add_feature/add_transcript” operation will now warn the
user that proceed will delete the feature
- data adapter grouping (see FASTA adapter)
- adding/updating PubMed ID will now show the publication title for
confirmation
- improved add_transcripts_from_gff3_to_annotations.pl
- adding of different annotation types (gene, pseudogene, tRNA, snRNA,
snoRNA, ncRNA, rRNA, miRNA, repeat_region, transposable_element)
- adding GO terms now supports searching/autocompletion
- annotation info editor now requests data from the server in batch mode
(should improve speed)
Fixes:
- Chado featureprop writeback for generic attributes
- add_transcripts_from_gff3_to_annotations.pl now properly loads status
attributes
- attributes being lost after undo/redo
- redo of a merge_transcript operation after deleting one of the
transcripts *should* work now
- properly handle dragged transcripts that contain UTR elements
- compressed data sent to the client no longer causes the client to hang
when there are too many annotations
- rewrote much of the split_transcript operation to better handle gene
splitting
(via Ed Lee on the WebApollo mailing list)
Posted to the GMOD News on
2013/11/22
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