Bug fixes

• Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.
• Fixed an issue with the advanced table filter functionality that prevented the removal of empty entries from columns expected to contain text.
• Fixed an issue where Excel formatted files (.xls, .xlsx) could not be imported as Trim Adapter Lists.
• Fixed a license issue causing workbenches to not start properly on Turkish Operating Systems.
• Fixed issue causing the license assistant dialog and EULA dialog to be too big for smaller screens. 
• Fixed an issue where weblinks to Uniprot sequences led to the homepage.

Advanced notice

With a release planned for late 2018, only 64 bit versions of the CLC Main Workbench will be made available. 32 bit versions will be discontinued from that time.

If you are concerned about this change, please contact our Support team ([email protected]).

Improvements and new features

• Workbenches without a license can now be run in Viewing Mode. In this mode, data can be viewed, imported and exported. Plugins needed for viewing certain data types can be installed. Viewing mode, with its added functionalities, replaces Limited Mode.
• A dialog is now presented on startup if there are installed workflows that need to be updated before they can be run. The information about what to do to when a workflow needs to be updated has been improved.
• The history of a data element can now be exported as a CSV format file.
• Changed amino acids colors to better suit users with various forms of color blindness.
• The Download Pfam Database tool now downloads version 31. Updates can now be made independently of the release of CLC Main Workbench, so the version available for download could change over time from the one recorded here.
• In table views, it is now possible to filter columns with the filters "Is in list" and "Is not in list" when the values are numbers.
• Importing a GO annotation file with the Standard Import tool, specifying the format "Generic annotation file for expression data", now fails with an informative warning if any of the GO annotations are truncated.
• Warnings are now reported if truncated GO annotations are found when opening data created by the Create Expression Browser tool.
• The 'Expression Browser Table' (output from the Create Expression Browser tool) now preserves sorting when changing the grouping, if sorting is not on any of the grouped columns.
• All wizard steps are now shown in the wizard sidebar when starting a tool or workflow.
• Visualization of features that wrap around the origin of circular sequences has been improved for sequences.
• Table filtering and search now interpret thousands and decimal separators in the same manner as the displayed table. Previously US punctuation was always used. This change means that if a table displays numbers in the form "123.456,7" then it is possible to find numbers less than ten by searching for "< 10,0" or "<10", but not "<10.0". If the table displays numbers in the form "123,456.7" then it is possible to find numbers less than ten by searching for "<10.0" and "<10", but not "<10,0".
• When a tool is disabled in a right-click context menu, hovering the mouse over the tool name will now reveal why a tool was disabled in most cases.
• The help window can now be closed by pressing the escape key.
• HTML formatting tags are now removed during export of data to Excel .xlsx or .xls format. This change does not affect the export of hyperlinks.
• A warning message is now presented when the tool Extract Sequences is run with the "Extract to single sequences option" selected and more than 100 sequences would result.

Changes

• The Search for Sequences at NCBI tool now uses accession.version identifiers instead of GI numbers, as GI numbers are being phased out by NCBI (see https://ncbiinsights.ncbi.nlm.nih.gov/2016/07/15/ncbi-is-phasing-out-sequence-gis-heres-what-you-need-to-know/. )
• Scrolling in a table now scrolls a fixed number of pixels, and not a fixed number of rows or columns.
• The "Help" and "Reset" buttons in pop-up dialogs are now buttons with text labels. They were previously buttons with icons.
• The GCG sequence exporter has been removed. The GCG alignment exporter is unaffected by these changes.
• Upgraded NCBI blast executables to version 2.6.0 for 64-bit systems. 32-bit systems still use version 2.2.30.

Bug fixes

• Fixed an issue where filtering a log for a job that was still running would result in error dialogs.
• Fixed an issue that had previously prevented configuration of the export option "Output as single file" in workflows.
• Fixed an issue where data exported with gzip or zip compression did not have the .gz or .zip suffix appended to the filename when earlier exports had been made with the same name and export location specified.
• Fixed an issue that could cause exports of reports with line graphs to fail.
• Fixed a bug where a cell containing multiple hyperlinked URLs caused export to Excel 2010 or Excel 97-2007 format to fail. Such cell contents are now written in plain text.

Plugin Notes

• Licenses for commercial modules are no longer required to install a module on a Workbench nor to view data generated by tools of a commercial module.
• The flexibility associated with network module licenses has been improved. Workbench module licenses provided via a CLC License Server are now initially loaded only when a tool provided by that module is launched. Such licenses are returned when 4 hours lapses since the last module tool was launched from that Workbench.

Advanced Notice

With a release planned for late 2018, only 64 bit versions of the CLC Main Workbench will be made available. 32 bit versions will be discontinued from that time.