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Latest improvements in CLC Main workbench

CLC Main Workbench 7.6.1

Release date: April 16, 2015

 

New features and improvements

  • BLAST has been upgraded to BLAST+ 2.2.30 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.2.30 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777
  • The GTF exporter is now available for the Main Workbench.
  • Transcriptomics experiment and sample tables can now be sorted, even with large numbers of rows.
  • Improved Excel, HTML and tab delimited export of variants (Choose only the annotations/columns you need).

Bug fixes

  • Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
  • Fixed an error affecting the "Cut Sequence Before/After Selection" tool in the Cloning editor.
  • Fixed bug where a left-click quickly followed by right-click was interpreted as double-click on OS X (in the persistence search result list, in the toolbox tree, and in the workflow editor).

CLC Main Workbench 7.6

Release date: February 24, 2015

New features and improvements

  • Tracks:
    • Consistent output when enriching variant tracks and annotation tracks with extra table columns. Output tracks from these tools now have the same number of added table columns and the columns will always be in the same order. Previously, if an added column had empty values for all variant rows, it would have been removed from the final table, resulting in varying number and relative order of additional columns when multiple samples were processed with the same tools/workflows. All columns are retained now, facilitating downstream processing of exported tables, and providing immediate visual reference as to which enrichment/annotation tools have been applied, even if they did not produce any results for a particular sample.
    • Tables for variant tracks and annotation tracks can now sort and filter columns with cells containing multiple numbers.
    • Improved the track viewer for variant tracks to show the sequence alteration on the rendered variant.
    • Graph tracks now show negative values filled upwards to y=0 (as expected).
    • Increased decimals for numbers when exporting table to CSV, tab delimited text, and Excel.
    • Improved reporting of errors related to low disk space.
  • Workflows:
    • When installing a workflow in the workflow manager, the newly installed workflow is automatically selected.
    • The "Run" button in the workflow editor does not require a saved workflow anymore to be enabled.
    • In the execution wizard of a workflow the "Reset to default" button is now active.
    • All icons in the workflow editor are now on the left side.
    • Introduction of snippets: Parts of workflows can now be saved as a snippet and reused in other workflows.
    • Installed workflows: It is now possible to create a copy of an installed workflow and open the copy in the view area by clicking once and then right-clicking on the installed workflow in the toolbox. This brings up the option "Open Copy of Workflow".
  • New features for the 3D molecule viewer:  
    • Align to Existing Sequence makes it possible to connect a 3D protein chain to a sequence, sequence list, or an existing alignment.
    • Transfer Annotations makes it possible to create atom groups from sequence annotations (and vice versa) for connected sequences.
    • Improved layout of the property viewer.
    • Improved PDB import of water molecules, DNA/RNA, and saccharides.
    • When importing PDB files, the resulting Molecule Project now contains citation information (PDB ID and primary reference), which can be found in the 'Show History' view.
  • MA plots, scatter plots and histograms can now accept expression tracks as input.
  • Batching: Processes tab and analysis execution logs now display batch names in addition to analysis names for enhanced clarity.
  • The External Application Client Plugin is now available directly from the Workbench Plugin Manager.

 

Bug fixes

  • Fixed display problem in read mappings showing too many hidden insertions (as vertical black lines) in certain overlapping paired reads.
  • Fixed problem with links and text in tables that were being cut off when succeeding a link.
  • Restriction site analysis: The values "Cut position(s)" column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
  • Workflows:
    • In the workflow editor the "Reset to default" now always reverts to the right names.
    • In the workflow editor the validation is now correctly triggered when changing the configuration of an input element.
    • The workflow editor can now open workflows in which the graphical view of the workflow is corrupt.
    • Fixed an exception which could occur during workflow migration.
    • Data with the same name can now be bundled multiple times in a workflow installer.
    • Previously when a plugin contained custom actions and a workflow, the workflow could not be installed. This has been fixed.
    • Fixed problem with unlocked output names that previously could not be configured during execution of a workflow.
    • A workflow with configured data from a server is now automatically validated when connected to the server (when opened in the editor). Previously the workflow had to be closed and reopened first.
    • The original workflow file included in a workflow installer can now be exported directly without having to restart the workbench in advance.”
  • A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings.

  •  Fixed an error that could cause batch processing to open all results rather than saving them.

  • Fixed problem going back in the wizard for the "Find Binding Site and Create Fragments" tool.
  • Fixed error occurring when removing an unsaved reads track from a track list.
  • Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.
  • Fixed error when showing protein translations of annotations shorter than 3 bases.
  • Search for PDB Structures at NCBI has been fixed to correctly show PDB deposit date and organism type.
  •  Fixed a bug that in some cases caused an error when annotating read sequence lists with the GFF/GTF/GVF annotation tool. 
  • Hypergeometric test on annotations: Fixed a rare error that occurred for some datasets containing annotations of the form: '1234 // abc'.
  • The alignment editor view and alignment primer design view now have independent settings. 

 

Plugin updates and bug fixes

  • TRANSFAC Plugin updated and now has two modes of operation: "Classic" and "Genomic". Classic mode is the legacy mode taking sequences as input and annotating these sequences. The new Genomic mode takes regions on a genome (an annotations track) as input. In addition, in both modes it is now possible to specify global thresholds of similarity score which can be used to filter the annotations included in the output.
  • A bug has been fixed with import of metadata containing column names with colons in the Metadata Import plugin.

CLC Main Workbench 7.5.2

Release date: April 15, 2015

Bug fixes

  • Fixed an error affecting the "Cut Sequence Before/After Selection" tool in the Cloning editor.
  • Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.

CLC Main Workbench 7.5.1

Release date: October 28, 2014

New features and improvements

  • It is now possible to run a workflow without an optional input.

Bug fixes

  • The AAC tool did not annotate variants in 3' UTR with their DNA-level change using the HGVS c.xxx format. This affects any analysis done with Gx 7.5 or earlier based on ENSEMBL CDS tracks from older versons. The AAC analysis should be redone using Gx 7.5.1 for correct annotation.

  • Pfam filtering bug fixed. Previously, Pfam only reported the first domain of each type in a query and as a consequence many domains were missed. We recommend that users whose research depends on Pfam annotations re-run the tool on their data.
  • Fixed a bug in the 'Maximum Likelihood Phylogeny' tool that failed when generating bootstrap values for certain input alignments.
  • Fixed problem with scrolling to the relevant files when selecting objects as parameters in tool wizards.
  • The Blast text results have been improved so they show the correct query and subject positions regardless of strand.
  • Fixed a problem that prevented BLAST operations when choosing to run these on the CLC Server.
  • It is now possible to run a workflow without an optional input.

CLC Main Workbench 7.5

Release date: August 28, 2014

New features and improvements

  • Workflows:
    • The input information is now shown in the preview dialog and also exported to all formats.
    • It is now possible to edit the workflow input name by right-clicking on the input name in the workflow.
    • Workflows as such can have multiple inputs (though this will disable the batch functionality).
    • Data can now be directly bundled with a workflow installation. This means that reference data can be packed and shared together with a workflow (only recommended for small data).
    • A workflow input can be pre-configured. If kept unlocked, it can be used to give a default when executing the workflow.
    • A text field has been added to the side panel, where you can search for elements in the workflow. A found element will be centered and highlighted.
    • A new editor was added to the workflow to make it easier to check the configuration. The new editor can be accessed from the lower left corner of the View Area and lists all configuration parameters.
    • Workflows can be packaged with a plugin and will get installed with the plugin simultaneously.
    • Workflows installed on the server now have an overlay icon in the workbench, to make them easily distinguishable from workflows installed in the workbench.
    • The execution of a workflow in the workbench and on the server have been unified to have the same behavior regarding logs, intermediate results and output naming.

    • Locked settings in the workflow wizard are now again hidden per default when executing the workflow, to give a cleaner, simpler look to the configuration. When expanding, all parameters are displayed.

  • Protein Analysis, Pfam domain search:
    • Pfam Domain Search now uses HMMER3 and the latest Pfam database that can be downloaded with the new tool "Download Pfam Database".
    • Searching multiple sequences is significantly faster.
    • New filters are available in the improved Pfam Domain Search tool to enable generation of the same results as the online tool.

  • 3D Molecule Viewer:
    • Protein Structure Alignment - high quality structural alignment of whole protein chains or selected regions of a protein, available from the Side Panel of Molecule Projects.
    • Project Tree improvements - new ways of selecting nearby atoms. Improved visualization of intermolecular bonds. Atom groups are now stored on the Molecule Project and can be renamed. Labels on custom atom groups now show residue names if applicable.
    • New molecule color scheme where only the carbon atom color is varied.
    • 3D view state - all 3D visualization settings (including custom atom groups) can now be stored on a molecule project and shared with others.
    • Molecule Preparation. Many improvements, including better handling of partial charges and more recognized chemical groups.
  • Local Search enabled from the menu bar now includes filtering on "Path".
  • Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
  • Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments and read mappings.
  • The tracks info panel, with track names in the left side of the track, now wraps information instead of showing a scroll bar.
  • Saving/applying side-panel settings for tables now works for different tables that share some columns. 
  • Copy operations can now be stopped.
  • Output from "Reverse Translate" can now be a Sequence List.

  • Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.

  • CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
  • Improved error message in the Empirical Analysis of DGE tool in case of invalid expression values in experiments (occurs rarely).
  • More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.
  • Genetic codes: The list of NCBI translation tables has been expanded to include  translation table 25 "Candidate Division SR1 and Gracilibacteria" (See: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c).
  • Improved error messages due to low disk space.

 

Bug fixes

  • Translation of CDS annotations to protein sequences was wrong in cases where the reading frame was not +1 or -1 in CDS annotations imported from ENSEMBL. This error affected the Translate to Protein tool, translation functionality in sequence viewers and their context menus, as well as the Amino Acid Consequences (AAC) variant annotation tool. We highly recommend redoing the AAC analysis for correct variant annotation, as CDS tracks typically are created from ENSEMBL data.
  • The right-click menu on certain annotations in tracks was not working when viewing a single track. This has been fixed.
  • Icons in the workflow editor are now scaled consistently when zooming in or out.
  • Several issues with the validation display in the workflow editor have been fixed.
  • A bug has been fixed in the workflow configuration wizard. Previously the input was not taken into account when deciding which parameters were enabled.
  • Fixed problem where the "space" key did not trigger "Find Conflict" in the stand-alone read mapping editor.
  • Fixed stand-alone read mappings not showing mismatches and insertions in the overflow graph.
  • 'Replace input sequences with result' in Cloning Editor no longer fails.
  • Multi-sequence BLAST search results (BLAST tables) are now exportable as plain text.
     

Changes

  • Due to upgrade to Java 7,  Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.

CLC Main Workbench 7.0.3

Release date: May 14, 2014
  • Fixed error that caused selections in views not to be centered in the middle of the view.
  • Fixed bug that caused a crash in the Reassemble Contigs tool
  • Fixed bug that made the Workbench crash when viewing tables under certain circumstances
  • Fixed problem with "Find" on stand-alone read mappings with a circular reference and sequence lists containing circular sequences.
  • Fixed problem with some parts of workflow not being executed if there was multiple branches in workflow.
  • CLC Main Workbench 7.0.1

    Release date: March 14, 2014New features and improvements
    • Fasta export:
      • Fasta export with trimming is now much faster and consumes less memory
      • Fasta export now reports progress while executing
      • When the "Remove trimmed regions" option is set, the Fasta export will ignore sequences in which all nucleotides are covered by a Trim annotation
    • Translate to Protein (Batch Process):
      • The wizard now has options for specifying whether to translate the coding regions or extract translations from the annotations
      • The log has been made more detailed and informative
      • If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
      • If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields
    • The PDB importer has improved support for custom residues

    Bug fixes

    • Fixed missing icon for "Metadata Import" in the phylogenetic tree table
    • Multi BLAST results table: the missing "Description (E-value)" field is displayed again in the table output
    • Fixed a bug that made PDB import fail on workstations with Turkish Locale settings
    • The tool "Restriction Site Analysis" ignored the selected number of cut sites in GWB 7.0. This has been fixed

    CLC Main Workbench 7.0

    Release date: February 11, 2014

    New features and improvements

    • New functionality for phylogenetic trees (was previously part of a beta plugin)

      • Greatly enhanced viewer for visualizing and working with phylogenetic trees. The viewer allows the user to rapidly create high-quality, publication-ready figures of the trees.

      • Large trees are made easy to explore using different zoom functionalities and a small minimap of the entire tree. The viewer also comes with two alternative tree layouts, namely circular layouts and radial layouts, which are great for visualizing very large trees.

      • Supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees.

      • Tool to reconstruct phylogenetic trees based on k-mers. This approach avoids the computationally intensive step of constructing a multiple alignment of the input sequences. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely related.
      • Tool performing a statistic evaluation of different substitution models to be used with maximum likelihood tree construction. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood.

      • Added an option for using the Kimura 80 substitution model when creating trees with distance based methods.
      • Distance-based tree reconstruction methods can now reconstruct trees from protein alignments using the Jukes-Cantor substitution model or the Kimura protein ML distance estimate.
      • A user defined start tree can now be supplied to the ML inference tool.
    • Complete redesign of the graphical user interface including:
      • New tool bar graphics
      • New product logos and colors, including splash screen
      • New background graphics on canvas and in dialogs
      • Tool bar has been re-organized
      • New tab design. Aligning the look and feel across platforms, which is particularly important to mac-users as split screen used to take up a lot of screen space.
    • New concept for Side Panels and Views:
      • Support for multiple screens: views can be moved to a different screen by dragging the tab of the view
      • Side Panels now consist of palettes that can be organized in group and the order can be customized
      • Palettes can be detached and placed anywhere on the screen
      • Navigation Area and Toolbox can be minimized to allow more pixels for displaying data
    • Zoom tools redesign:
      • The zoom tools have been re-organized and placed closer to the data
      • A zoom slidershows the present zoom level and can be used to adjust zoom
        • Detailed zoom is a new feature that allows zooming in and out in very small increments by dragging the zoom slider and moving the cursor above it. An expert feature for e.g. large tracks.

      • New zoom tools. Easy adjustment of zoom speed for improved zooming of huge sequences.

      • Detachable Side Panel editors. A Side Panel editor can be dragged from the main workbench window and dropped outside the workbench, making a separate window e.g. on a second screen, if available.

    • Copying data in the Navigation Area runs much faster and uses less memory than before. This is a great improvement which also kicks in when moving data between a CLC Genomics Server and a Workbench.

    • Workflows:
      • Possibility to have bulk configuration of elements. This enables to set the same reference data for multiple elements at once.
      • Workflows can be added inside a workflow. The inner workflow is "unfolded" into the single elements.
      • Parameters can now be renamed in the editor by the creator during configuration of the elements.
      • Workflows with invalid/unknown elements are laid out nicer and more consistent.
      • The sidepanel has now an option to display rulers in the editor to indicate better the size of a workflow (particularly when exporting)
      • Fit Width now fits the entire workflow in the editor by zooming out.
      • The sidepanel has a new section "Minimap" which shows an outline of the whole workflow. It allows to navigate the workflow in the view and also supports zooming
      • One can change the design of the workflow editor via the sidepanel (removed the old designs in the preferences)
      • Better validation when configuring parameters in workflows
      • If a tool receives inputs from at least two tools, the inputs can now be ordered via the context menu on the connections or the input part of the target element.
      • The name of an output in the workflow can be set by configuring the output element
      • Parameters of a workflow run can now be exported to various formats via the wizard
      • It is now possible to reset a reference parameter. Before it was only possible by removing the whole element and add it again.
      • In the workbench the installed workflows are now sorted alphabetically.
      • The graphics export of a workflow now knows about the scale and one can now export the whole workflow or only the current view.
      • A cpw file can now be dragged into the workflow manager and will be installed.
      • Further speed improvements on working with larger workflows in the editor
      • New tools that are now workflow-enabled:
    • 3D structure viewer:
      • Property viewer - a new tab in the Side Panel. Shows detailed information about the atom under the mouse pointer. If multiple atoms are selected (Ctrl-click), the distance (two atoms selected), angle (three atoms selected), dihedral angle (four atoms selected) formed by the selected atoms, is shown in the Property viewer. If a molecule is selected in the Project Tree, meta-data relating to the molecule is shown in the Property viewer.
      • Issues List. Issues related to the molecule structures and their chemistry representation is listed in the Issues List view on Molecule Projects. If seen in split-view with the 3D viewer, a selected issue will zoom to the atoms involved in the issue and select them in the 3D view.
      • General improvements to the PDB importer
      • Double-clicking an entry in the Project Tree will zoom-to-fit on the molecule or atom group.
      • When selecting atoms (by mouse clicking or from sequence), the atom context (whole residue or molecule) will also be shown in the 3D view. From context menu on 'Current' selection, an atom group can be generated either from the exact selection or from the selection plus the context (whole residues or molecules).
    • Extract consensus sequence is now able to copy annotations from both existing consensus sequence and the reference sequence.
    • When extracting consensus sequence from a mapping, conflict and low coverage annotations now include the position on the reference.
    • Trim annotations can be used to trim off sequences when exporting to fasta.
    • Secondary peak calling has been improved: it now only detects peaks that have a distinct peak shape, only peaks that fall within the same interval as the top peak are called. In addition, trim annotations are taken into account so that no peaks are called within trimmed regions. This greatly reduced false positive calls. Finally, the annotations now include information about the secondary peak's fraction of the maximum peak height. 
    • Advanced table filter now includes an option to search for "starts with" in addition to just "contains"
    • Limitations on export of Excel 2010 files (xlsx) are removed:
      • Multiple tables can be exported to one xlsx file
      • Reports can be exported to xlsx
      • Hyperlinks are preserved in xlsx files
    • SignalP prediction has been updated to be server-, batch- and workflow enabled.
    • Folder contents view: subfolders will display how many items they have
    • Assemble Sequences tools now accept sequence lists as input.
    • REBASE restriction enzyme list updated to version 310.

     

    Bug fixes

    • Workflow:
      • In the editor the "Fit Width" zooming was active, but behaved as "100%" zooming. Therefore the "100%" zooming is now active instead of the "FitWidth"
      • Added or connected elements are now placed near where you connect or add them, even when zoomed near or far.
      • It was possible to Undo the action of adding a workflow output, but it was not possible to Redo afterwards.
      • The right-hand icons in an element now scale with zooming.
      • The log of a workflow run on the server contains now the same information as when run in the workbench.
      • When configuring elements in the editor, the "Reset to CLC Standards" button is now functional and will reset the parameters to their default values. When configuring during installation or execution the button is disabled.
      • The log of a server executed workflow now states when the workflow has been cancelled.
      • A workflow with elements which provide additional inputs could not be batched.
    • Crash when adding data to experiments (e.g. by running any of the statistical analysis tools) has been fixed.
    • Various bugs in the extract consensus sequence tool have been fixed.
    • When translating to protein, ambiguous nucleotides potentially resulting in stop codons were not translated properly, and only the codons resulting in an amino acid were represented in the protein. Now the stop codons are also represented by an X in the protein sequence.
    • A problem with filtering and sorting the BLAST output table has been solved. Some of the columns were treated as text instead of numeric.
    • Restriction maps, histogram data, and primer tables could not be exported to csv or similar. This has been fixed.

    • When using the “Find Open Reading Frame” tool, the input sequence was reported incorrectly in the ORF table. This has been fixed.

    • Fixed problems with Excel export that failed when special characters were used in the name.

    Changes

    • The two tools in the "Multiplexing" folder in the toolbox category have been changed:
      • "Process Tagged Sequences" has been removed..
      • "Sort Sequences by Name" has been moved directly into the Sequencing Data Analysis folder.
    • Motif search: annotations created by the motif search are of type "Motif" instead of "Region"

    CLC Main Workbench 6.9.2

    Release date: January 23, 2014

    Bug fixes

    • Fixed: Error message when running analysis on experiments (statistical tests, clustering etc.)
    • The folder used by the Workbench for storing log and settings files on Windows 8 has been updated to follow conventions for Windows 8 which is identical to Windows 7. Any existing settings will be copied to the new location automatically. 
    • Fixed various problems related to launching the Workbench through Java Webstart.
    • Fixed: Opening a search view for searching sequences at NCBI would sometimes fail.
    • Fixed various stability and performance problems of Maximum likelihood phylogeny.
    • Fixed problem that caused a crash with extract consensus sequence tool with certain parameter configurations and with read mappings with no reads.
    • Fixed a bug in the Assemble Sequences tool causing some data sets to produce inferior contigs.

    CLC Main Workbench 6.7

    Release date: August 9, 2012

    New features

    Workflow

    • Workflows can be built in the Workbench to combine various tools from the Toolbox into one analysis, connecting the output from one tool to the input from another
    • In the first release, the gateway cloning tools are the only tools that can be incorporated into workflows.
    • Workflows can be distributed and installed either in the Workbench or in the CLC Genomics Server
    • The creator of the workflow can configure parameters for the workflow and these will be fixed when the workflow is distributed and installed
    • The creator of the workflow decides which of the output from the tools that should be saved and which should be discarded
    • Workflows can be run in batch, making it a powerful tool for crunching high numbers of samples through the same pipeline.

    Plugin updates

    Grid integration plug-in is integrated into the general server plug-in. If a grid preset is present on the server, the Grid option becomes available in the Workbench dialog.

    Old Releases

    View older releases in our CLC Main Workbench release archive