Latest improvements for CLC Genomics Server

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CLC Genomics Server 8.5.5

Release date: 2017-06-08

Server specific

  • Fixed an issue that caused the import of Wiggle and USCS chromosome band files to fail on CLC Genomics Server setups.
  • More detailed feedback is now presented in the Plugins tab of the web administrative client when there are issues with installed plugins, such as missing or expired licenses or version incompatibility.

Shared with workbenches

Improvements

  • When importing tracks, the history of the track now contains the full path name of the imported file.

Bug fixes

Compatibility

  • CLC Genomics Workbench 9.5.5 is the corresponding client for CLC Genomics Server 8.5.5.
  • Biomedical Genomics Workbench 3.5.5  is the corresponding client for CLC Genomics Server 8.5.5.
  • CLC Command Line Tools 3.5.5 is the corresponding client for CLC Genomics Server 8.5.5.

We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 9.5.4, 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.4, 3.5.3, 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.4, 3.5.3, 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to CLC Genomics Server 8.5.5. In addition, CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can  connect to a CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

 

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for CLC Genomics Server 8.5.5.

Compatibility

CLC Command Line Tools 3.5.5 is the corresponding client for CLC Genomics Server 8.5.5.

CLC Command Line Tools 3.5.5 can also act as a client for the CLC Genomics Server 8.5.4, 8.5.3, 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server. 



CLC Genomics Server 8.5.4

Release date: 2017-02-14

Bug fixes

  • A timeout value that would lead a job to fail after 24 hours, which was introduced as part of optimizations to run on multiple threads in the CLC Genomics Server 8.5 has been extended to 7 weeks. The tools affected are Annotate from Known Variants, Filter against Known Variants, Filter against Control Reads, Annotate with Exon Number, Annotate with Flanking Sequences, Filter Marginal Variant Calls, Compare Sample Variant Tracks, Trio Analysis, GO enrichment Analysis, Amino Acid Changes, Annotate with Conservation Score, Predict Splice Site Effect, Link Variants to 3D Protein Structure, Merge Annotation Tracks, Create Statistics for Target Regions, Fisher Exact Test, Annotate with Overlap Information, Filter Based on Overlap, Filter Reference Variants, Identify Candidate Variants, Coverage Analysis, and InDels and Structural Variants.
  • Fixed an issue in the RNA-Seq Analysis tool where running in EM mode, with a "Strand specific" setting of "Forward" or "Reverse" would result in the second read of a pair mapped as a broken pair being counted incorrectly if that read was mapped outside a region annotated as a transcript.
  • Fixed an issue where an error arose when using the RNA-Seq Analysis tool with the EM option and a strand specific setting of "Forward" or "Reverse" in cases where the second read of mapped broken pair mapped to the opposite strand of the strand specific setting.
  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the forward and/or reverse count for a longer variant, supported by paired reads with both children having the same direction, could be too low. The forward count and reverse count is now reported correctly.
  • Fixed an issue with the InDels and Structural Variants tool where an incorrect insertion could be called when the optimal alignment of a read's unaligned end around the breakpoint included a gap in the insertion sequence.
  • Fixed an issue in the InDels and Structural Variants tool that would terminate analysis of large read mappings prematurely a fraction of the times.
  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the count and read count could be reported as marginally higher than they actually were in a small minority of cases. For the affected variants, this could then also result in variant frequencies being reported that were slightly higher than they should have been, in some cases above 100%. Variants affected by this issue are a small subset of variants where the variant affected overlapped another potential variant and where only the affected variant was then reported. This change could lead to a small decrease in the number variants reported compared to earlier versions of the CLC software, due to a variant no longer passing the count or read count filtering constraints. The impact of this change is expected to be low. For example, in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after this fix was implemented.
  • Fixed an issue where the Basic Variant Detection, Fixed Ploidy Variant Detection, Low Frequent Variant Detection and Local Realignment tools could fail if a deletion was encountered at the end of a match between a read and the reference in the mapping used as input.
  • Fixed an issue in the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequent Variant Detection tools where the tools could stop with an error. The problem arose when a read split up within a mapping (e.g. to map to separate exons) was split into 4 or more parts, and at least 4 of those parts would map within a region of adjacent variants being considered as a possible multiple nucleotide variant (MNV). This infrequent problem was most likely to occur when using high coverage RNA-Seq mappings and looking for variants occurring at low frequency. It was introduced in the previous bugfix release of the CLC Genomics Server, version 8.5.3.
 

Specific to Biomedical enabled Genomics Server

  • A timeout value that would lead a job to fail after 24 hours, which was introduced as part of optimizations to run on multiple threads in the CLC Genomics Server 8.5 has been extended to 7 weeks. The tools affected are Add Information from Variant Databases, Remove Variants Found in External Database, Remove Germline Variants, Add Exon Number, Add Flanking Region, Remove False Positives, Identify highly Mutated Gene Groups and Pathways, Add Information About Amino Acid Changes, Add Conservation Scores, Identify Variants with Effect on Splicing, Link Variants to 3D Protein Structure, QC for Targeted Sequencing, Identify Enriched Variants in Case vs Control Samples, Add Information from Overlapping Genes, Add information from Genomic Regions, Add Information from Overlapping Variants, Remove Variants Outside Genome Genome Regions, Remove Variants Outside Target Regions, Remove Variants Inside Genome Regions, Identify Mutated Genes, Remove Reference Variants, and Whole Genome Coverage Analysis.

Compatibility

  • CLC Genomics Workbench 9.5.4 is the corresponding client for CLC Genomics Server 8.5.4.
  • Biomedical Genomics Workbench 3.5.4  is the corresponding client for CLC Genomics Server 8.5.4.
  • CLC Command Line Tools 3.5.4 is the corresponding client for CLC Genomics Server 8.5.4.
We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 9.5.3, 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.3, 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.3, 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to CLC Genomics Server 8.5.4. In addition, CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can  connect to a CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.  

Advanced notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in March, 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in March, 2017.
  • Support for some older operating systems (OS), listed below, will be discontinued in March, 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. If you are concerned about the proposed change, please contact our Support team ([email protected]), letting them know the OS being used and the products you are running on that OS.
    • 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

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for CLC Genomics Server 8.5.4.

Compatibility

CLC Command Line Tools 3.5.4 is the corresponding client for CLC Genomics Server 8.5.4. CLC Command Line Tools 3.5.4 can also act as a client for the CLC Genomics Server 8.5.3, 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.


CLC Genomics Server 8.5.3

Release date: 2016-12-14

Bugfixes and Improvements

For the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools, the following have been addressed:
  • Fixed an issue where the coverage of a longer variant that contained another variant was reported for both the longer variant and the contained variant. The coverage for the contained variant is now reported correctly.
  • Fixed an issue affecting coverage calculation for SNVs without immediately adjacent variants when using paired read data: if the second read of a pair containing the variant did not meet the requirements of the quality filter, neither the first nor second read of that pair contributed to the coverage calculated for the variant.
  • Fixed an issue where, for an SNV without immediately adjacent variants, overlapping reads of a pair that had conflicting base calls for that variant position contributed to the values calculated for coverage, read coverage, and read count of that variant.
  • Fixed a bug where count, read count, and forward- and reverse read count could be incorrect for variants found in overlapping regions of a pair of reads and where the variant was originally identified as being adjacent to one or more other variants.

The above issues, including information on the products affected, are described on the public notification page: Coverage and count reporting for variants in certain circumstances are incorrect

For the Identify Known Mutations from Sample Mappings tool, the following issues have been addressed:
  • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where reads in a sample mapping were not identified as supporting the presence of a known variant in cases where the first position of the variant region in the mapped read contained a gap.
  • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where a read containing a variant longer than a known variant being tested for was counted as supporting the known variant in cases where the first part of the read’s variant sequence is identical to that of the known variant.
  • Fixed an issue in the Identify Known Mutations from Sample Mappings tool where overlapping reads of a pair having conflicting base calls for a variant position could contribute to the coverage calculated for that variant.

Compatibility

  • CLC Genomics Workbench 9.5.3 is the corresponding client for CLC Genomics Server 8.5.3.
  • Biomedical Genomics Workbench 3.5.3  is the corresponding client for CLC Genomics Server 8.5.3.
  • CLC Command Line Tools 3.5.3 is the corresponding client for CLC Genomics Server 8.5.3.
We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 9.5.2, 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3,5.2, 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.2, 3.5.1, 3.5, 3.0.1 and 3.0 can connect to CLC Genomics Server 8.5.3. In addition, CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can  connect to a CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

Advanced notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in spring, 2017.
  • 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. If you are concerned about the proposed change, please contact our Support team ([email protected]), letting them know the OS being used and the products you are running on that OS.
    • 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

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for CLC Genomics Server 8.5.3.

Compatibility

CLC Command Line Tools 3.5.3 is the corresponding client for CLC Genomics Server 8.5.3. CLC Command Line Tools 3.5.3 can also act as a client for the CLC Genomics Server 8.5.2, 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.  


CLC Genomics Server 8.5.2

Release date: 2016-10-25

Improvements

  • SRA download functionality has been updated to support the upcoming NCBI transition to HTTPS.

Bug fixes

  • Fixed an issue with running BLAST on macOS Sierra.
  • Updated PFAM links reported by the Pfam Domain Search tool.

Compatibility

  • CLC Genomics Workbench 9.5.2 is the corresponding client for CLC Genomics Server 8.5.2.
  • Biomedical Genomics Workbench 3.5.2  is the corresponding client for CLC Genomics Server 8.5.2.
  • CLC Command Line Tools 3.5.2 is the corresponding client for CLC Genomics Server 8.5.2.
We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 9.5.1, 9.5, 9.0.1 and 9.0, Biomedical Genomics Workbench 3.5.1, 3.5, 3.0.1 and 3.0, and CLC Command Line Tools 3.5.1, 3.5, 3.0.1 and 3.0 can connect to CLC Genomics Server 8.5.2. In addition, CLC Genomics Workbench 9.5.x and Biomedical Genomics Workbench 3.5.x and CLC Command Line Tools 3.5.x can  connect to a CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

Advanced Notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in spring, 2017.
  • 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. If you are concerned about the proposed change, please contact our Support team ([email protected]), letting them know the OS being used and the products you are running on that OS.
    • 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

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for CLC Genomics Server 8.5.2.

Compatibility

CLC Command Line Tools 3.5.2 is the corresponding client for CLC Genomics Server 8.5.2. CLC Command Line Tools 3.5.2 can also act as a client for the CLC Genomics Server 8.5.1, 8.5., 8.0.1 and 8.0. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.


CLC Genomics Server 8.5.1

Release date: 2016-09-28

Genomics Server

Bug fixes

Compatibility

  • CLC Genomics Workbench 9.5.1 is the corresponding client for CLC Genomics Server 8.5.1.
  • Biomedical Genomics Workbench 3.5.1  is the corresponding client for CLC Genomics Server 8.5.1.
  • CLC Command Line Tools 3.5.1 is the corresponding client for CLC Genomics Server 8.5.1.
We recommend running the corresponding versions of clients for CLC Genomics Server. However, CLC Genomics Workbench 9.5, 9.0 and 9.0.1, Biomedical Genomics Workbench 3.5, 3.0 and 3.0.1, and CLC Command Line Tools 3.5, 3.0 and 3.0.1 can connect to CLC Genomics Server 8.5.1. In addition, CLC Genomics Workbench 9.5.1, Biomedical Genomics Workbench 3.5.1 and CLC Command Line Tools 3.5.1 can  connect to a CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

CLC Server Command Line Tools

This is a compatibility release to supply the corresponding client for the CLC Genomics Server x.x.x.

Compatibility

CLC Command Line Tools 3.5.1 is the corresponding client for CLC Genomics Server 8.5.1. CLC Command Line Tools 3.5.1 can act as a client for the CLC Genomics Server 8.5, 8.0 and 8.0.1. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.


CLC Genomics Server 8.5

Release date: 2016-09-15

Server specific

Improvements

General

  • Support for special characters in AD passwords has been added.
  • Added workflow grid job dependency support for Univa Grid Engine.
  • When unlocked parameters of a workflow installed on a server are edited, the name of the person to last change that workflow and the date and time of the change are now presented above the design in the thin client.
  • To ensure that correct server information is available, grid jobs can no longer be launched on setups where the host name and port are not set in the "Job distribution" area of the thin client on the master server. A check for these settings has been added to the "check setup" functionality of the server.

External Applications

  • When changes are made to an External Applications configuration, the name of the person who made that change and the date and time the change was made is available in a tooltip when the cursor is placed over the name of that External Application in the thin client.

Bug fixes

  • Fixed an issue where the server web administration interface failed to accept certain passwords containing non-ASCII characters.

Shared with Workbenches

New tools and features

  • "Search for Reads in SRA ..." allows search and download of reads from the SRA database.
  • "Identify Known Mutations from Sample Mapping " can be used to look up known genomic variants in read mappings.
  • "Identify Candidate Variants " can be used to identify and extract variants that fulfill certain criteria.
  •  A new GFF3 importer is available as an option in the Import -> Tracks tool.
  • A new option "Use EM estimation (recommended)" was added to the RNA-Seq Analysis tool. This enables the use of an expectation-maximization algorithm to distribute ambiguous reads between isoform/genes.
  • A new option in the Sample Reads tool makes it possible to choose whether sampling should be deterministic or random.

Improvements

General

  • The Local Realignment tool has a new option that can allow the use of guidance variants longer than 100bp.
  • The InDels and Structural Variants tool now offers the option to include reads mapped as broken pairs in the analysis.
  • The InDels and Structural Variants tool offers now the option for consensus calculation to ignore reads if their relative coverage or quality scores are too low.
  • The Identify Graph Thresholds tool can now be run using only a lower or upper threshold limit, rather than having to specify both.
  • The Identify Graph Thresholds tool can now be configured to work on specified regions only.
  • The Trim Sequences tool now handles ambiguity codes in the adapter/primer sequences.
  • All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
  • Standard deviations in reports are now being calculated with a different algorithm than previously. This will have no noticeable effect in the overwhelming majority of cases.
  • Improved performance of a number of tools when run on systems with multiple cores: Annotate from Known Variants, Filter against Known Variants, Filter against Control Reads, Annotate with Exon Number, Annotate with Flanking Sequences, Filter Marginal Variant Calls, Compare Sample Variant Tracks, Trio Analysis, GO enrichment Analysis, Amino Acid Changes, Annotate with Conservation Score, Predict Splice Site Effect, Link Variants to 3D Protein Structure, Merge Annotation Tracks, Create Statistics for Target Regions, Fisher Exact Test, Annotate with Overlap Information, Filter Based on Overlap, Identify Candidate Variants, and Filter Reference Variants.
  • It is now possible to export expression tracks in BED format. The expression value will be exported as the score.
  • The COSMIC importer has been updated to support the latest version of the COSMIC database, release v77.
  • The tools "Filter Based On Overlap" and "Annotate with Overlap Information" now work with the Statistical Comparison Tracks produced by the Advanced RNA-Seq plugin.
  • When importing metadata from a spreadsheet with formulas in it, the result of the evaluation of the formula (as displayed in Excel) is now imported rather than the formula itself.
  • GenBank import now also allows for file names with 'GBFF' extension.
  • Improved the progress reporting for the import of large, gzip compressed Illumina and Ion-Torrent files.
  • The Extract Consensus Sequence tool now outputs a sequence list for all results. Previously, when running this tool directly, if the result was a single sequence, it would output a sequence, not a sequence list. (Nothing has changed when this tool is run as part of a workflow, where sequence lists were always generated.)
  • General speed and usability improvements.

Biomedical-enabled Servers only

  • A RefSeq reference data set is now available in the reference data manager.
  • Improved performance of a number of tools when run on systems with multiple cores: Add Information from Variant Databases, Remove Variants Found in External Database, Remove Germline Variants, Add Exon Number, Add Flanking Region, Remove False Positives, Identify highly Mutated Gene Groups and Pathways, Add Information About Amino Acid Changes, Add Conservation Scores, Identify Variants with Effect on Splicing, Link Variants to 3D Protein Structure, QC for Targeted Sequencing, Identify Enriched Variants in Case vs Control Samples, Add Information from Overlapping Genes, Add information from Genomic Regions, Add Information from Overlapping Variants, Remove Variants Outside Genome Genome Regions, Remove Variants Outside Target Regions, Remove Variants Inside Genome Regions, Identify Mutated Genes, and Remove Reference Variants.

Bug fixes

  • Fixed an issue with the tools "Extract from Selection" and "Extract Reads Based on Overlap" so that they now correctly extract mapped reads that extend over the (arbitrarily chosen) ends of the 1D representation of a circular genome.
  • Fixed an issue where the Motif Search tool was incorrectly reporting all match accuracies as either 0% or 100%.
  • Fixed a bug where exporting to Wiggle on systems with specific system locales would produce files that could not be re-imported.
  • Fixed an issue that caused characters in sequence names to be rendered incorrectly when a report was exported to Excel.
  • The Find Binding Sites and Create Fragments tools now properly display mismatches when the primer input is in lower-case.
  • Fixed a memory leak in the Extract Consensus Sequence tool.
  • Fixed an issue where sequences of length zero would cause the Create BLAST Database tool to throw an error. Such sequences are now skipped and will not included in the final database.
  • The Illumina High-Throughput Sequencing Import tool now correctly warns that zip files with multiple entries are not supported.
  • Various minor bugfixes.

Plugin updates and retirements

All CLC Genomics Servers

Compatibility

  • CLC Genomics Workbench 9.5 is the corresponding client for the CLC Genomics Server 8.5.
  • Biomedical Genomics Workbench 3.5  is the corresponding client for the CLC Genomics Server 8.5.
  • CLC Command Line Tools 3.5 is the corresponding client for the CLC Genomics Server 8.5.
We recommend running the corresponding versions of clients for the CLC Genomics Server.However, CLC Genomics Workbench 9.0 and 9.0.1, Biomedical Genomics Workbench 3.0 and 3.0.1, and CLC Command Line Tools 3.0 and 3.0.1 can connect to the CLC Genomics Server 8.5. In addition, the CLC Genomics Workbench 9.5, Biomedical Genomics Workbench 3.5 and CLC Command Line Tools 3.5 can can connect to a CLC Genomics Server 8.0.x. Tools that have changed between versions cannot be launched when using compatible, but not corresponding, client-server combinations.

Notice

From now on, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these are discontinued.

Advance Notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools are scheduled to be removed from the Server and CLC Genomics Workbench in spring, 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and CLC Genomics Workbench in spring, 2017.

CLC Server Command Line Tools

New tools

Analysis related tools

  • download_sra                                 SRA Download
  • identify_candidate_variants_new   Identify Candidate Variants  (Existing tool for Bx-enabled servers now enabled on all servers)
  • mutation_tester_tool                      Identify Known Mutations from Sample Mappings (Existing tool for Bx-enabled servers now enabled on all servers)

Tools for server maintenance

  • disable_maintenance_mode     Disable server maintenance mode
  • enable_maintenance_mode     Enable server maintenance mode
  • install_plugin_and_restart         Install plugins and restart the server
  • install_workflow                        Install a workflow
  • list_plugins                               Lists installed plugins
  • list_workflows                           Lists installed workflows
  • restart_server                           Restart server and any attached job nodes
  • shutdown_server                     Shut down the server
  • uninstall_plugin_and_restart    Uninstall plugin(s) and restart the server
  • uninstall_workflow                    Uninstall workflow         

Improvements

  • Workflow outputs can now be configured so that subfolders to contain the outputs are created.
  • New placeholders are available when defining the names of exporter outputs:  {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}.
  • Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.
  •  
  • Added support for running workflows that exposed custom parameter names containing underscores.
  • When using the {2} placeholder for custom naming in workflow output elements, only unlocked inputs will be included in the generated name.
  • Improved validation of the VCF exporter such that more meaningful error messages are presented.

Tools with added parameters

  • graph_threshold
    • Added options:
      • --masking-mode
      • --region-track
      • --use-lower-threshold
      • --use-upper-threshold
  • local_realignment
    • Added option:
      • --max-extrinsic-variant-length
  • rna_seq
    • Added option:
      • --em-enabled
  • sample_reads
    • Added option:
      • --sample-type
  • structural_variant_detection
    • Added options:
      • --broken-pairs
      • --min-consensus-coverage
      • --min-qscore

Bugfixes

  • Fixed an issue so that the download_pfam_database can now be run using the CLC Command Line Tools. Associated with this is the removal of the -i , --input parameter for this tool.

Compatibility

CLC Command Line Tools 3.5 is the corresponding client for CLC Genomics Server 8.5.  CLC Command Line Tools 3.5 can act as a client for the CLC Genomics Server 8.0 and 8.0.1. However, we recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.

Notice

From now on, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these are discontinued.


CLC Genomics Server 8.0.1

Release date: 2016-06-07

Improvements

  • When running a workflow on a CLC Genomics Server with grid nodes and using the classic job queuing option, the name of individual subjobs contains the name of the workflow element being run. Previously,  "Grid Executer" was the name reported for each subjob.

Bug fixes

  • Fixed an issue with the RNA-Seq Analysis tool that could arise when the "Genomes annotated with genes and transcripts" option was chosen: If two or more genes had the same name, and a transcript could be assigned to each from the mRNA track, then the value in the "Transcripts annotated" column in the GE track and in the TE track was 0. Furthermore, all counts for such genes were reported as zero, even when there were reads mapping to them.
  • Fixed an issue that prevented workflows containing an input modifying element but no outgoing connection from being run on the server.
  • Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.

Compatibility

  • CLC Genomics Workbench: CLC Genomics Workbench 9.0.1 and 9.0 can connect to the CLC Genomics Server 8.0.1. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, CLC Genomics Workbench 9.0.1 with CLC Genomics Server 8.0.1.
  • Biomedical Genomics Workbench:  Biomedical Genomics Workbench 3.0.1 and 3.0 can connect to a CLC Genomics Server 8.0.1 that has a Biomedical Genomics Server Extension license. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, Biomedical Genomics Workbench 3.0.1 with CLC Genomics Server 8.0.1.
  • CLC Command Line Tools. CLC Command Line Tools 3.0.1 and 3.0 can act as clients for the CLC Genomics Server 8.0.1. We generally recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server. Here, CLC Command Line Tools 3.0.1 with CLC Genomics Server 8.0.1.

Advanced notice

  • From the autumn 2016 release, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.
  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.

CLC Server Command Line Tools 3.0.1

Compatibility release

CLC Command Line Tools 3.0.1 is the corresponding client for CLC Genomics Server 8.0.1. CLC Command Line Tools 3.0.1 and 3.0 can act as clients for the CLC Genomics Server 8.0.1. However, we generally recommend running the corresponding version of the CLC Command Line Tools CLC Genomics Server.


CLC Genomics Server 8.0

Release date: 2016-03-31

Server specific

New features

  • The Server can be configured such that all steps of a Workflow will be executed on the same node in a job node or grid node setup.
  • The health and throughput of the CLC Server can now be monitored using any monitoring software that supports the JMX standard.
  • Options are now available for how direct data transfer from client systems is handled, including the ability to disable transfers.  This affects where temporary data is held when transferring client-side data into Server locations and enables administrative control of Server data import initiated from either Workbench or CLC Command Line Tools.
  • Multiple post-processing steps can now be configured for External Applications, allowing the re-import or other post-processing of multiple outputs from third party tools.
  • The Create Scatter Plot tool can be run on the CLC Genomics Server.
  • The Create MA Plot tool can be run on the CLC Genomics Server.

Improvements

General

  • Audit log presentation and searching has been improved. Improvements include the ability to search for failed tasks and for entries between specified time points.
  • Host addresses and "Canonical host name" are now presented as suggestions for the master node host in the Server setup area of the web administrative interface.
  • Reporting of system level problems has been added to the Status and Maintenance area of the web administrative interface.
  • Workflows are now sorted alphabetically by name in the web administrative interface
  • It is now possible to choose which LDAP bind is used for selected LDAP operations
  • Improved the wording of the status messages on the server maintenance pages.

External Applications

  • Post process algorithm parameters are made available for user configuration by unlocking them via the "Edit and map parameters" editor.
  • Linking post process algorithm parameters to "End user parameters" is now done via the "Edit and map parameters" editor
  • "End user parameters for post processing only" are no longer necessary.
  • When available, the name for inputs used by a post-processing tool is presented in the "Edit and map parameters" editor, rather than the earlier generic input name ("Input data (common for all algorithms)").

Changes

  • The options formerly in the job queuing options group under the Job distribution area are now in an area called job running options.
  • The parameter graph view of External Applications has been removed.

Bug fixes

  • Fixed an issue observed on job node setups where consecutive tasks of a workflow executed on the same job node could result in a cached data object being used as input rather than fetching a new copy, which could lead to errors being reported.
  • Fixed an issue with built-in authentication on job node setups where any new user added while a job node was down would not be persisted through a Genomics Server restart.
  • Fixed an issue where if a job node addition failed, that same job node could not be added within the same Server session.
  • Fixed an issue where files on the server could not be moved or copied if the plugin that created them was not installed on the server.
  • Fixed an issue where a Workbench could attempt to retrieve data from a Server before the Server login process had completed.
  • Fixed a bug where doing automatic association using a metadata table stored on a CLC Server would fail.

Shared with Workbenches

Improvements

RNA-seq related

  • The RNA-Seq Analysis tool now computes Transcripts Per Million (TPM) values.
  • Faster analysis of multiple samples in the RNA-Seq Analysis tool due to caching of reference index files.
  • Performance improvements for Expression Tracks in RNA-Seq.
  • Expression tracks now contain links to external databases when available.
  • Transcript level expression tracks now contain the gene name for each transcript.

Mapping related

Track related

  • The tool Create Mapping Graph can now create a coverage graph over the start positions of reads in a read mapping.
  • Improved error messaging when trying to import malformed fasta files into tracks.

Metadata related

  • The use of partial or exact matching schemes can be chosen when associating data with metadata using the Associate Data Automatically option.

General

  • Fixed an issue with the VCF-exporter resulting in inconsistent information being output to the exported VCF. The metadata field "##reference" field now contains a human readable string-representation identifying the reference genome the exported variants are based on. The metadata field "##fileOrigin" was added to contain a human readable string-representation identifing the exported variant track.
  • Performance optimization for sizing phylogenetic trees by metadata.
  • The 3D Protein Structure Database has been updated.
  • The Download Pfam Database tool has been updated to download version 29.
  • Substantial speed improvements to BAM export.
  • 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.
  • SAM records with CIGAR strings with no aligned residues can now be handled when importing SAM/BAM files.
  • GFF Track Import now supports spaces in annotation names

Changes

Workflow related

General

  • The naming rules for the outputs of several tools have been changed to align with those applied by most other tools. The tools affected by these changes are: Local Realignment, Low Frequency Variant Detection, Fixed Ploidy Variant Detection, Basic Variant Detection as well as the legacy variant detection tools: Probabilistic Variant Detection and Quality-based Variant Detection.
  • The BaseQRankSum value for variants is now negative to indicate that the qualities for the variant is below those for the reference allele. The BaseQRankSum is now calculated as a positive value when the qualities for the variant are above those for the reference allele.
  • Export to clc format now truncates very long filenames.
  • Versions of individual tools are now reported in the history of output objects.
  • For the NGS importers, the paired reads minimum and maximum default interval has been updated to 1 - 1000.
  • Plots without any data points will now be skipped when rendering reports.
  • The annotations "Known variation", "Validated by other experiment", "Ancestral allele", and "Phenotype related", created by variant track import are not used and have therefore been removed from variant tracks.
  • The Detailed Mapping Report statistics table and the QC for Read Mapping statistics table now show previously missing values for regions with partial coverage. For fully covered regions these values cannot be calculated, and empty strings are replaced with coverage minimum, average and standard deviation. Numeric sorting is retained by inserting NaN values instead of empty strings, where calculations cannot be made.
  • RPM package installers for Linux are no longer available.
  • Associate Data Automatically accepts data elements (not folders) as input.

Bug fixes

    • BED Export: when exporting block list entries (such as connected exons from mRNA tracks), positions were absolute, but are now relative to the 'chromStart' position.
    • Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
    • Fixed an off-by-one error for read start positions in the 'Find Broken Pair Mates...' output table.
    • Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
    • Fixed an issue where an error was reported if the local realignment tool detected an insertion followed by a deletion in the original mapping. Such positions are now ignored.
    • Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
    • Fixed a bug that led to the creation of an empty folder for each excluded batch unit.
    • Added missing percentage signs for identities and gaps in Blast text exports.
    • When the InDels and Structural Variants tool is added to the workflow the "P-value Threshold" parameter did not show up in the Select settings wizard step under "Significance of unaligned ends breakpoints". This has been fixed.
    • Fix 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.
    • The "Extract and Count" tool in Small RNA analysis now only accepts sequences and sequence lists. Previously, it incorrectly accepted standalone read mappings or small RNA samples as well.
    • A bug was fixed where no BaseQRankSum was calculated for insertions of length 1.

Plugin updates and retirements

All CLC Genomics Servers

      • A new RNA-Seq analysis plugin is now available: Advanced RNA-Seq
      • Annotate with GFF: Now supports spaces in annotation names.
      • The RNA-Seq Legacy plugin has been retired.

Biomedical-enabled Servers only

      • Ingenuity Variant Analysis: Enforce diploid export has been exposed in the wizard and switched on as default option,in the drop-down options for “Analysis pipeline name”, “Personal genome” has been renamed to “Single sample”, and fixed an issue where the IVA plugin failed when it was given a genome with a non-circular MT chromosome.
      • QIAGEN GeneRead Panel Analysis Plugin: Adjusted a number of parameter settings in the workflow and moved the workflow to the subfolder "Somatic cancer (TAS)" under "Targeted Amplicon Sequencing".
Compatibility
      • CLC Genomics Workbench 9.0. The CLC Genomics Workbench 9.0 connects to the CLC Genomics Server 8.0.
      • Biomedical Genomics Workbench 3.0.  The Biomedical Genomics Workbench 3.0 connects to the the CLC Genomics Server 8.0 with a Biomedical Genomics Server Exension.
      • CLC Command Line Tools. The CLC Command Line Tools 3.0 connects to the CLC Genomics Server 8.0.

Advanced notice

From the autumn 2016 release, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.

CLC Server Command Line Tools

New features and improvements

New Tools

      • ma_plot       Create MA Plot
      • xy_scatter_plot       Create Scatter Plot

Tools that have changed parameters

All Genomics Servers

      • associate_metadata     Associate Metadata Added option:   --match-scheme
      • contig_read_mapping Added option:  --match-cost
      • mapping_graph_tracks   Create Mapping Graph Tracks Added option:  --reads-start-coverage
      • read_mapping     Map Reads to Reference Added option:  --match-cost

Bug fixes - Commands replaced

These replacements apply to Biomedical Genomics Server Extension users only

      • add_link_to_structure   Please use link_to_structure to run the Link Variants to 3D Protein Structure tool.
      • download_3d_structure_information_db    Please use download_sequence_to_structure_dbto run the Download 3D Protein Structure Database tool.

Commands removed

    • chip_seq      ChIP-Seq Analysis (legacy)
    • identify_candidate_variants     Identify Candidate Variants (legacy)


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