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CLC Server

This document assumes that a licensed copy of CLC Genomics WorkBench 22 is installed locally and available to the user.

Before You Begin

Email scinet_vrsc@USDA.GOV so that the admins can setup the import/export directories and permissions for access.

We need the following information:

  1. Path to your project directory.
  2. Do you need access to the mem nodes for your CLC workflow?

CLC Server Login

  1. File -> Connections -> CLC Server Connection
  2. Server Name and Port
  • If connecting via VPN/OCVPN
    Server name:
    Server port: 7777
  • If connecting via ARS Network
    Server host:
    Server port: 7777
    1. Username and Password(GA code not required)
  1. Log in.

screenshot of CLC Genomics Workbench 22.0.2 software homescreen

After successful login, you should see a directory CLC-<your project> in the top left window.

CLC Server vs GRID

screenshot of CLC Genomics Workbench 22.0.2 Server Options

CLC provides two ways to offload jobs - CLC Server and GRID. Both serve different purposes.

CLC Server can only be used to perform Standard Import and Export. These tasks are performed on Ceres DTN node for faster transfer rate.

Note that if users select “CLC Server” for any tasks other than those mentioned below, those tasks will not execute and will remain paused.

GRID can be used to run compute tasks on Ceres nodes.

The table below lists the tasks and option to use

Category Utilities Option
Export   CLC Server
Import   CLC Server
Search for Reads in SRA   GRID
Classical Sequence Analysis    
  Create Alignment GRID
  K-mer Based Tree Construction GRID
  Create Tree GRID
  Model Testing GRID
  Maximum Likelihood Phylogeny GRID
  Extract Sequences GRID
  Motif Search GRID
  Translate to Protein GRID
  Convert DNA to RNA GRID
  Convert RNA to DNA GRID
  Reverse Complement Sequence GRID
  Find Open Reading Frames GRID
  Download Pfam Database GRID
  Pfam Domain Search GRID
  Find and Model Structure GRID
Molecular Biology Tools    
  Trim Sequences GRID
  Assemble Sequences GRID
  Assemble Sequences to Reference GRID
  Secondary Peak Calling GRID
  Find Binding Sites and Create Fragments GRID
  Add attB Sites GRID
  Create Entry clone (BP) GRID
  Create Expression clone (LR) GRID
  Download BLAST Databases GRID
  Create BLAST Database GRID
Prepare Sequencing Data    
  QC for Sequencing Reads GRID
  Trim Reads GRID
  Demultiplex Reads GRID
Quality Control    
  QC for Targeted Sequencing GRID
  QC for Read Mapping GRID
  Whole Genome Coverage Analysis GRID
  Combine Reports GRID
  Create Sample Report GRID
Resequencing Analysis    
  Map Reads to Reference GRID
  Local Realignment GRID
  Merge Read Mappings GRID
  Remove Duplicate Mapped Reads GRID
  Extract Consensus Sequence GRID
  Basic Variant Detection GRID
  Fixed Ploidy Variant Detection GRID
  InDels and Structural Variants GRID
  Identify Known Mutations from Mappings GRID
  Copy Number Variant Detection (CNVs) GRID
  Filter against Known Variants GRID
  Remove Marginal Variants GRID
  Remove Homozygous Reference Variants GRID
  Remove Variants Present in Control Reads GRID
  Annotate from Known Variants GRID
  Remove Information from Variants GRID
  Annotate with Conservation Scores GRID
  Annotate with Exon Numbers GRID
  Annotate with Flanking Sequences GRID
  Annotate with Repeat and Homopolymer Information GRID
  Identify Enriched Variants in Case vs Control Samples GRID
  Identify Shared Variants GRID
  Trio Analysis GRID
  Create Variant Track Statistics Report GRID
  Amino Acid Changes GRID
  Predict Splice Site Effect GRID
  GO Enrichment Analysis GRID
  Download 3D Protein Structure Database GRID
  Link Variants to 3D Protein Structure GRID
RNA-Seq and Small RNA Analysis    
  RNA-Seq Analysis GRID
  PCA for RNA-Seq GRID
  Differential Expression in Two Groups GRID
  Differential Expression for RNA-Seq GRID
  Create Heat Map for RNA-Seq GRID
  Create Expression Browser GRID
  Create Venn Diagram for RNA-Seq GRID
  Gene Set Test GRID
  Quantify miRNA GRID
  Annotate with RNAcentral Accession Numbers GRID
  Create Combined miRNA Report GRID
  Extract IsomiR Counts GRID
Microarray Analysis    
  Create Box Plot GRID
  Principal Component Analysis GRID
  Proportion-based Statistical Analysis GRID
  Gaussian Statistical Analysis GRID
  Create MA Plot GRID
  Create Scatter Plot GRID
  Create Histogram GRID
Epigenomics Analysis    
  Histone ChiP-Seq GRID
  Transcription Factor ChIP-Seq GRID
  Annotate with Nearby Gene Information GRID
  Map Bisulfite Reads to Reference GRID
  Call Methylation Levels GRID
  Create RRBS-fragment Track GRID
  Learn Peak Shape Filter GRID
  Apply Peak Shape Filter GRID
  Score Regions GRID
De Novo Sequencing    
  De Novo Assembly GRID
  Map Reads to Contigs GRID
Utility Tools    
  Extract Annotated Regions GRID
  Merge Overlapping Pairs GRID
  Extract Reads GRID
  Merge Annotation Tracks GRID
  Merge Variant Tracks GRID
  Convert to Tracks GRID
  Convert from Tracks GRID
  Filter on Custom Criteria GRID
  Annotate with Overlap Information GRID
  Filter Annotations on Name GRID
  Filter Based on Overlap GRID
  Create GC Content Graph GRID
  Create Mapping Graph GRID
  Identify Graph Threshold Areas GRID
  Update Sequence Attributes in Lists GRID
  Split Sequence List GRID
  Subsample Sequence List GRID
  Rename Elements GRID
  Rename Sequences in Lists GRID
Legacy Tools    
  Compare Sample Variant Tracks (legacy) GRID
  Empirical Analysis of DGE (legacy) GRID