-includes Trinotate report summary statistics and web report.
-custom search results are only reported for blastp or blastx (not assuming both were performed).
minor patch release, no change in functionality.
removed ' set -eou pipefail ' for now.
included pull req: changes $FindBin::Bin to $FindBin::RealBin to deal w/ resolving symlinks
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.
-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.
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.
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).
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.