Bug fixes

• Fixed an issue with running BLAST on macOS Sierra.
• Updated PFAM links reported by the Pfam Domain Search tool.
• Fixed a problem where launching a tool from the Quick Launch window after sorting led to the wrong tool being started.
• Various minor bugfixes.

Advanced Notice

Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed.

• • Windows: Windows Vista and Windows Server 2008
  • Mac: Mac OS X 10.7 and 10.8
  • Linux:  Red Hat Enterprise Linux 5, SUSE Linux Enterprise Server 10 and 11 and Fedora 6 through 21

New tools

Import Metadata - basic and easy metadata import. This tool supplements the tools available in the Metadata Table Editor.

Improvements

Metadata

• The use of partial or exact matching schemes can be chosen when associating data with metadata using the Associate Data Automatically option.
• It is now possible to change the type of a metadata column, even if it already contains values. Conversion is only possible when all existing values in the given column can be converted to the new data type.
• Usability enhancements in the Metadata Table Editor.

Workflow

• Workflow inputs  can now be ordered via the Workflow Editor, affecting the order that input information is requested when setting up a Workflow run.
  • Workflows with multiple input elements, where all input elements will be changed per batch, can now launched in batch by right-clicking on the installed workflow name and choosing the option "Run in Batch Mode...".
• Tools in a Worfklow that have been renamed will have both the new tool name and the original tool name displayed in the Workflow Configuration Editor.

General

• Performance optimization for sizing phylogenetic trees by metadata.
• The Find Structure Database has been updated. Please use the Download Find Structure Database tool to work with the latest version.
• The Download Pfam Database tool has been updated to download version 29.
• The options for saving the output from "batch jobs" have been improved. Outputs can now be saved into a specified single folder in addition to the other established save options.
• All Excel sheets in a document are now imported and each sheet has a table created for its contents.
• The CSV, HTML and Excel table/tabular exporter now use "Inf" and "NaN" values to replace the ambiguous "?".
• In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading.
• An option has been added to allow the same print settings to be applied to all reports being exported to pdf format in a given export run.
• The "Manage Resources" tab has been removed from the the Plugin Manager.

Changes

General

• Versions of individual tools are now reported in the history of output objects.
• Export to clc format now truncates very long filenames.
• Plots without any data points will now be skipped when rendering reports.
• RPM package installers for Linux are no longer available.
• Associate Data Automatically accepts data elements (not folders) as input.
• The 'Database Fields' label shown in the 'Show Element Info' view has been renamed to ' Local Attribute Fields'.
• The "Metadata Role Override" parameter that was visible when creating Workflows has been removed.
• The user can no longer uncheck "export all columns" for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.

Bug fixes

• Fixed a bug when the download buttons on BLAST result table view failed for nucleotide sequences.
• Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
• Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
• Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
• Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
• Fixed an issue where the "Show results"option in the Processes tab would lead to an error if the results dataset was very large.
• Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.
• Fixed an issue where an error arose when renewing a borrowed network license.
• Fixed a bug that led to the creation of an empty folder for each excluded batch unit.
• Fixed a bug that  led to the inclusion of the number of excluded batch units in the count of the total number of batch units to be processed.
• Added missing percentage signs for identities and gaps in Blast text exports.
• A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error.
• Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
• An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
• Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
• Fixed an issue with Open Copy of Workflow so it now works on all workspaces rather than just the first workspace.
• Fixed an issue that could lead to an error when a job status description changed while a full description was being generated.
• Fixed an issue with handling dates when importing metadata from Excel format files using the Metadata Table Editor.
• Fixed a bug that was causing missing report text lines
• Fixed an issue where, when the option to "Skip these updates" was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated.
• Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
• Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
• Fixed an issue where sub-jobs were not resumed after pausing and resuming a batch process.
• Fixed an issue where the workflow installer creation keyboard shortcut could be used when it should have been disabled.
• Fixed a rare issue that could be triggered by switching editor view with a double click.

Plugin updates and fixes

All plugins need to be installed in the new Workbench for compatibility reasons.

Changes to freely available plugins

• Batch rename: Fixed an issue where a warning was displayed for entries not modified.