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Changelog.txt
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## Trinotate Release v3.2.1 (Apr 9, 2020)
-updated eggnog url to a fixed resource as per PR
## Trinotate Release v3.2.0 (Aug 7, 2019)
-separate columns are now output for gene ontology based on blastx or blastp results.
-misc. minor bugfixes
## Trinotate v3.1.0 (Oct 24, 2017)
-includes Trinotate report summary statistics and web report.
-custom search results are only reported for blastp or blastx (not assuming both were performed).
## Trinotate v3.0.2 Release (Mar 3, 2017)
minor patch release, no change in functionality.
developer notes:
removed ' set -eou pipefail ' for now.
included pull req: changes $FindBin::Bin to $FindBin::RealBin to deal w/ resolving symlinks
## Trinotate v3.0.1 Release (Apr 12, 2016)
Includes updates to the report table output formatter to better ensure column alignment w/ results, and removing any tab or newline chars in annotations that would go into the tab-delimited fields and cause offsets.
## Trinotate v3.0.0 Release (2016-03-09)
-updated resources based on currently available data (swissprot, pfam, go, etc.)
-incorporating Kegg annotations
-including auto-trinotate to facilitate computations and database loading.
-support for lighttpd as the webserver for TrinotateWeb
-releasing the boilerplate database build process, in case anyone ever wants to roll their own based on the latest swissprot, pfam, etc.
-dropping explicit support for Trembl
-added custom database search functionality. If you want trembl, just search it as a custom database.
-updated sample data using latest version of Trinity assembly and functional analysis computations.
## Trinotate Release 2.0.2 (April 30, 2015)
TrinotateWeb components are updated for improved compatibility with the new Trinity identifiers (TR|c...)
The run_mongoose_server.sh, when given any command line arguments, will use a locally installed version of canvasXpress libraries. By default, it uses them live over http from the main canvasXpress site.
## Trinotate v2.0.1 (Feb 6, 2015)
double-clicking on a gene/transcript graph point opens up a new window instead of replacing the current volcano or MA plot page (which is intensive to draw).
Trinotate v2.0.0 (Feb, 2015)
Database resources are updated to Jan,2015 versions of UniProt (swissprot and uniref90), PFam, and GO.
A single sqlite boilerplate database is provided with both swissprot and uniref90 support.
The mongoose webserver is now recommended for use with TrinotateWeb
TrinotateWeb has been heavily refined, with a facelift and related engineering spearheaded by Leonardo Gonzalez.
## v1.1 Trinotate, pre-2.0 release (Jan 29, 2015)
post-migration from sourceforge
Includes Leonardo Gonzalez's UI overhaul and query optimizations
######################################################################################
########## Releases below were on Sourceforge before we moved to Github ############
######################################################################################
## Release: 2014-07-08
-added support for Uniref90 in addition to swissprot.
-updated boilerplate databases to use current TrEMBL and Swissprot dat files.
-updated Gene Ontology to current obo
-updated eggNog definitions to current
-incorporated Pfam2GO
## Release: 2013-11-10
-overhaul of sqlite loaders to use faster bulk loading of data.
-ability to incorporate custom sets of gene/transcript clusters for navigation using TrinotateWeb
-sqlite database name is parameterized so multiple different trinotate sqlite dbs can be used and stored in the same directory.
-various updates to the TrinotateWeb to improve data navigation
-use Trinotate instead of Trinotate.pl
## Release: 2013-08-26
Trinotate:
-added BLASTX for transcript-based homology search, in addition to the BLASTP protein-based analyses
-added RNAMMER support to include rRNA transcript annotations/identification.
-expanded database structure to accommodate genome annotations and IGV integration (still in testing phase - to be further built out and incorporated into a future release).
TrinotateWeb:
-httpserver includes menu and can have port value set as the parameter. Also, can use local js or pull js over http
-sample/replicate blockings shown in heatmaps
-heatmap scaling can be user-adjusted.
-CanvasXpress upgrade
-cluster view: limit initial view to 50 randomly sampled genes for quicker interactive loading. User can reset the max to show.
## Release: trinotate_r20130706.tgz
Trinotate and TrinotateWeb migrated out of Trinity source and into separate sourceforge project.