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      • Minimum System Requirements
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      • Updating Partek Flow
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      • Dependencies
      • Docker and Docker-compose
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    • Live Training Event Recordings
      • Bulk RNA-Seq Analysis Training
      • Basic scRNA-Seq Analysis & Visualization Training
      • Advanced scRNA-Seq Data Analysis Training
      • Bulk RNA-Seq and ATAC-Seq Integration Training
      • Spatial Transcriptomics Data Analysis Training
      • scRNA and scATAC Data Integration Training
    • Tutorials
      • Creating and Analyzing a Project
        • Creating a New Project
        • The Metadata Tab
        • The Analyses Tab
        • The Log Tab
        • The Project Settings Tab
        • The Attachments Tab
        • Project Management
        • Importing a GEO / ENA project
      • Bulk RNA-Seq
        • Importing the tutorial data set
        • Adding sample attributes
        • Running pre-alignment QA/QC
        • Trimming bases and filtering reads
        • Aligning to a reference genome
        • Running post-alignment QA/QC
        • Quantifying to an annotation model
        • Filtering features
        • Normalizing counts
        • Exploring the data set with PCA
        • Performing differential expression analysis with DESeq2
        • Viewing DESeq2 results and creating a gene list
        • Viewing a dot plot for a gene
        • Visualizing gene expression in Chromosome view
        • Generating a hierarchical clustering heatmap
        • Performing biological interpretation
        • Saving and running a pipeline
      • Analyzing Single Cell RNA-Seq Data
      • Analyzing CITE-Seq Data
        • Importing Feature Barcoding Data
        • Data Processing
        • Dimensionality Reduction and Clustering
        • Classifying Cells
        • Differentially Expressed Proteins and Genes
      • 10x Genomics Visium Spatial Data Analysis
        • Start with pre-processed Space Ranger output files
        • Start with 10x Genomics Visium fastq files
        • Spatial data analysis steps
        • View tissue images
      • 10x Genomics Xenium Data Analysis
        • Import 10x Genomics Xenium Analyzer output
        • Process Xenium data
        • Perform Exploratory analysis
        • Make comparisons using Compute biomarkers and Biological interpretation
      • Single Cell RNA-Seq Analysis (Multiple Samples)
        • Getting started with the tutorial data set
        • Classify cells from multiple samples using t-SNE
        • Compare expression between cell types with multiple samples
      • Analyzing Single Cell ATAC-Seq data
      • Analyzing Illumina Infinium Methylation array data
      • NanoString CosMx Tutorial
        • Importing CosMx data
        • QA/QC, data processing, and dimension reduction
        • Cell typing
        • Classify subpopulations & differential expression analysis
    • User Manual
      • Interface
      • Importing Data
        • SFTP File Transfer Instructions
        • Import single cell data
        • Importing 10x Genomics Matrix Files
        • Importing and Demultiplexing Illumina BCL Files
        • Partek Flow Uploader for Ion Torrent
        • Importing 10x Genomics .bcl Files
        • Import a GEO / ENA project
      • Task Menu
        • Task actions
        • Data summary report
        • QA/QC
          • Pre-alignment QA/QC
          • ERCC Assessment
          • Post-alignment QA/QC
          • Coverage Report
          • Validate Variants
          • Feature distribution
          • Single-cell QA/QC
          • Cell barcode QA/QC
        • Pre-alignment tools
          • Trim bases
          • Trim adapters
          • Filter reads
          • Trim tags
        • Post-alignment tools
          • Filter alignments
          • Convert alignments to unaligned reads
          • Combine alignments
          • Deduplicate UMIs
          • Downscale alignments
        • Annotation/Metadata
          • Annotate cells
          • Annotation report
          • Publish cell attributes to project
          • Attribute report
          • Annotate Visium image
        • Pre-analysis tools
          • Generate group cell counts
          • Pool cells
          • Split matrix
          • Hashtag demultiplexing
          • Merge matrices
          • Descriptive statistics
          • Spot clean
        • Aligners
        • Quantification
          • Quantify to annotation model (Partek E/M)
          • Quantify to transcriptome (Cufflinks)
          • Quantify to reference (Partek E/M)
          • Quantify regions
          • HTSeq
          • Count feature barcodes
          • Salmon
        • Filtering
          • Filter features
          • Filter groups (samples or cells)
          • Filter barcodes
          • Split by attribute
          • Downsample Cells
        • Normalization and scaling
          • Impute low expression
          • Impute missing values
          • Normalization
          • Normalize to baseline
          • Normalize to housekeeping genes
          • Scran deconvolution
          • SCTransform
          • TF-IDF normalization
        • Batch removal
          • General linear model
          • Harmony
          • Seurat3 integration
        • Differential Analysis
          • GSA
          • ANOVA/LIMMA-trend/LIMMA-voom
          • Kruskal-Wallis
          • Detect alt-splicing (ANOVA)
          • DESeq2(R) vs DESeq2
          • Hurdle model
          • Compute biomarkers
          • Transcript Expression Analysis - Cuffdiff
          • Troubleshooting
        • Survival Analysis with Cox regression and Kaplan-Meier analysis - Partek Flow
        • Exploratory Analysis
          • Graph-based Clustering
          • K-means Clustering
          • Compare Clusters
          • PCA
          • t-SNE
          • UMAP
          • Hierarchical Clustering
          • AUCell
          • Find multimodal neighbors
          • SVD
          • CellPhoneDB
        • Trajectory Analysis
          • Trajectory Analysis (Monocle 2)
          • Trajectory Analysis (Monocle 3)
        • Variant Callers
          • SAMtools
          • FreeBayes
          • LoFreq
        • Variant Analysis
          • Fusion Gene Detection
          • Annotate Variants
          • Annotate Variants (SnpEff)
          • Annotate Variants (VEP)
          • Filter Variants
          • Summarize Cohort Mutations
          • Combine Variants
        • Copy Number Analysis (CNVkit)
        • Peak Callers (MACS2)
        • Peak analysis
          • Annotate Peaks
          • Filter peaks
          • Promoter sum matrix
        • Motif Detection
        • Metagenomics
          • Kraken
          • Alpha & beta diversity
          • Choose taxonomic level
        • 10x Genomics
          • Cell Ranger - Gene Expression
          • Cell Ranger - ATAC
          • Space Ranger
          • STARsolo
        • V(D)J Analysis
        • Biological Interpretation
          • Gene Set Enrichment
          • GSEA
        • Correlation
          • Correlation analysis
          • Sample Correlation
          • Similarity matrix
        • Export
        • Classification
        • Feature linkage analysis
      • Data Viewer
      • Visualizations
        • Chromosome View
          • Launching the Chromosome View
          • Navigating Through the View
          • Selecting Data Tracks for Visualization
          • Visualizing the Results Using Data Tracks
          • Annotating the Results
          • Customizing the View
        • Dot Plot
        • Volcano Plot
        • List Generator (Venn Diagram)
        • Sankey Plot
        • Transcription Start Site (TSS) Plot
        • Sources of variation plot
        • Interaction Plots
        • Correlation Plot
        • Pie Chart
        • Histograms
        • Heatmaps
        • PCA, UMAP and tSNE scatter plots
        • Stacked Violin Plot
      • Pipelines
        • Making a Pipeline
        • Running a Pipeline
        • Downloading and Sharing a Pipeline
        • Previewing a Pipeline
        • Deleting a Pipeline
        • Importing a Pipeline
      • Large File Viewer
      • Settings
        • Personal
          • My Profile
          • My Preferences
          • Forgot Password
        • System
          • System Information
          • System Preferences
          • LDAP Configuration
        • Components
          • Filter Management
          • Library File Management
            • Library File Management Settings
            • Library File Management Page
            • Selecting an Assembly
            • Library Files
            • Update Library Index
            • Creating an Assembly on the Library File Management Page
            • Adding Library Files on the Library File Management Page
            • Adding a Reference Sequence
            • Adding a Cytoband
            • Adding Reference Aligner Indexes
            • Adding a Gene Set
            • Adding a Variant Annotation Database
            • Adding a SnpEff Variant Database
            • Adding a Variant Effect Predictor (VEP) Database
            • Adding an Annotation Model
            • Adding Aligner Indexes Based on an Annotation Model
            • Adding Library Files from Within a Project
            • Microarray Library Files
            • Adding Prep kit
            • Removing Library Files
          • Option Set Management
          • Task Management
          • Pipeline managment
          • Lists
        • Access
          • User Management
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          • Orphaned files
        • Usage
          • System Queue
          • System Resources
          • Usage Report
      • Server Management
        • Backing Up the Database
        • System Administrator Guide (Linux)
        • Diagnosing Issues
        • Moving Data
        • Partek Flow Worker Allocator
      • Enterprise Features and Toolkits
        • REST API
          • REST API Command List
      • Microarray Toolkit
        • Importing Custom Microarrays
      • Glossary
    • Webinars
    • Blog Posts
      • How to select the best single cell quality control thresholds
      • Cellular Differentiation Using Trajectory Analysis & Single Cell RNA-Seq Data
      • Spatial transcriptomics—what’s the big deal and why you should do it
      • Detecting differential gene expression in single cell RNA-Seq analysis
      • Batch remover for single cell data
      • How to perform single cell RNA sequencing: exploratory analysis
      • Single Cell Multiomics Analysis: Strategies for Integration
      • Pathway Analysis: ANOVA vs. Enrichment Analysis
      • Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein
      • How to Integrate ChIP-Seq and RNA-Seq Data
      • Enjoy Responsibly!
      • To Boldly Go…
      • Get to Know Your Cell
      • Aliens Among Us: How I Analyzed Non-Model Organism Data in Partek Flow
    • White Papers
      • Understanding Reads in RNA-Seq Analysis
      • RNA-Seq Quantification
      • Gene-specific Analysis
      • Gene Set ANOVA
      • Partek Flow Security
      • Single Cell Scaling
      • UMI Deduplication in Partek Flow
      • Mapping error statistics
    • Release Notes
      • Release Notes Archive - Partek Flow 10
  • Partek Genomics Suite
    • Installation Guide
      • Minimum System Requirements
      • Computer Host ID Retrieval
      • Node Locked Installation
        • Windows Installation
        • Macintosh Installation
      • Floating/Locked Floating Installation
        • Linux Installation
          • FlexNet Installation on Linux
        • Installing FlexNet on Windows
        • License Server FAQ's
        • Client Computer Connection to License Server
      • Uninstalling Partek Genomics Suite
      • Updating to Version 7.0
      • License Types
      • Installation FAQs
    • User Manual
      • Lists
        • Importing a text file list
        • Adding annotations to a gene list
        • Tasks available for a gene list
        • Starting with a list of genomic regions
        • Starting with a list of SNPs
        • Importing a BED file
        • Additional options for lists
      • Annotation
      • Hierarchical Clustering Analysis
      • Gene Ontology ANOVA
        • Implementation Details
        • Configuring the GO ANOVA Dialog
        • Performing GO ANOVA
        • GO ANOVA Output
        • GO ANOVA Visualisations
        • Recommended Filters
      • Visualizations
        • Dot Plot
        • Profile Plot
        • XY Plot / Bar Chart
        • Volcano Plot
        • Scatter Plot and MA Plot
        • Sort Rows by Prototype
        • Manhattan Plot
        • Violin Plot
      • Visualizing NGS Data
      • Chromosome View
      • Methylation Workflows
      • Trio/Duo Analysis
      • Association Analysis
      • LOH detection with an allele ratio spreadsheet
      • Import data from Agilent feature extraction software
      • Illumina GenomeStudio Plugin
        • Import gene expression data
        • Import Genotype Data
        • Export CNV data to Illumina GenomeStudio using Partek report plug-in
        • Import data from Illumina GenomeStudio using Partek plug-in
        • Export methylation data to Illumina GenomeStudio using Partek report plug-in
    • Tutorials
      • Gene Expression Analysis
        • Importing Affymetrix CEL files
        • Adding sample information
        • Exploring gene expression data
        • Identifying differentially expressed genes using ANOVA
        • Creating gene lists from ANOVA results
        • Performing hierarchical clustering
        • Adding gene annotations
      • Gene Expression Analysis with Batch Effects
        • Importing the data set
        • Adding an annotation link
        • Exploring the data set with PCA
        • Detect differentially expressed genes with ANOVA
        • Removing batch effects
        • Creating a gene list using the Venn Diagram
        • Hierarchical clustering using a gene list
        • GO enrichment using a gene list
      • Differential Methylation Analysis
        • Import and normalize methylation data
        • Annotate samples
        • Perform data quality analysis and quality control
        • Detect differentially methylated loci
        • Create a marker list
        • Filter loci with the interactive filter
        • Obtain methylation signatures
        • Visualize methylation at each locus
        • Perform gene set and pathway analysis
        • Detect differentially methylated CpG islands
        • Optional: Add UCSC CpG island annotations
        • Optional: Use MethylationEPIC for CNV analysis
        • Optional: Import a Partek Project from Genome Studio
      • Partek Pathway
        • Performing pathway enrichment
        • Analyzing pathway enrichment in Partek Genomics Suite
        • Analyzing pathway enrichment in Partek Pathway
      • Gene Ontology Enrichment
        • Open a zipped project
        • Perform GO enrichment analysis
      • RNA-Seq Analysis
        • Importing aligned reads
        • Adding sample attributes
        • RNA-Seq mRNA quantification
        • Detecting differential expression in RNA-Seq data
        • Creating a gene list with advanced options
        • Visualizing mapped reads with Chromosome View
        • Visualizing differential isoform expression
        • Gene Ontology (GO) Enrichment
        • Analyzing the unexplained regions spreadsheet
      • ChIP-Seq Analysis
        • Importing ChIP-Seq data
        • Quality control for ChIP-Seq samples
        • Detecting peaks and enriched regions in ChIP-Seq data
        • Creating a list of enriched regions
        • Identifying novel and known motifs
        • Finding nearest genomic features
        • Visualizing reads and enriched regions
      • Survival Analysis
        • Kaplan-Meier Survival Analysis
        • Cox Regression Analysis
      • Model Selection Tool
      • Copy Number Analysis
        • Importing Copy Number Data
        • Exploring the data with PCA
        • Creating Copy Number from Allele Intensities
        • Detecting regions with copy number variation
        • Creating a list of regions
        • Finding genes with copy number variation
        • Optional: Additional options for annotating regions
        • Optional: GC wave correction for Affymetrix CEL files
        • Optional: Integrating copy number with LOH and AsCN
      • Loss of Heterozygosity
      • Allele Specific Copy Number
      • Gene Expression - Aging Study
      • miRNA Expression and Integration with Gene Expression
        • Analyze differentially expressed miRNAs
        • Integrate miRNA and Gene Expression data
      • Promoter Tiling Array
      • Human Exon Array
        • Importing Human Exon Array
        • Gene-level Analysis of Exon Array
        • Alt-Splicing Analysis of Exon Array
      • NCBI GEO Importer
    • Webinars
    • White Papers
      • Allele Intensity Import
      • Allele-Specific Copy Number
      • Calculating Genotype Likelihoods
      • ChIP-Seq Peak Detection
      • Detect Regions of Significance
      • Genomic Segmentation
      • Loss of Heterozygosity Analysis
      • Motif Discovery Methods
      • Partek Genomics Suite Security
      • Reads in RNA-Seq
      • RNA-Seq Methods
      • Unpaired Copy Number Estimation
    • Release Notes
    • Version Updates
    • TeamViewer Instructions
  • Getting Help
    • TeamViewer Instructions
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On this page
  • Filesystem and storage
  • Task queue and job processing
  • User quotas and limitations
  • Authentication settings
  • Email settings
  • General preferences
  • Additional Assistance

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  1. Partek Flow
  2. User Manual
  3. Settings
  4. System

System Preferences

PreviousSystem InformationNextLDAP Configuration

Last updated 7 months ago

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The System preferences menu accessible to administrator accounts (Figure 1) allows you to configure Partek Flow preferences. These preferences generally govern the activities of other users within the Partek Flow server. They can only be viewed and configured by Administrator accounts. The preferences are subdivided into the following sections:

  • Filesystem and storage

  • Task queue and job processing

  • User quotas and limitations

  • Authentication settings

  • Email settings

  • [General preferences](#general preferences)

Modifying preferences under the User quotas and limitations section require the User Disk Quotas enterprise license. Upon opening the system, all sections are collapsed except for Filesystem and storage (Figure 1).

Figure 1. System Preferences Page

Filesystem and storage

Data download directory

  • Specifies the directory on the server to which the data files will be uploaded

Library file directory

  • Specifies the directory on the server to which the library files will be uploaded

Default project output directory

  • If Sample file directory is selected, files will be written on the same directory in which the sample files are located

  • If Other is selected, a directory on the server must be specified to which the project output files will be written

  • The user can override this setting by specifying the output directory in the project’s Data tab after at least one sample has been created

  • If Enforced private directory is selected, files will be written on the user's private directory. The alternative folder specified after else will be used if no private directory is assigned to a user.

Store file-path symbolic links

  • If Yes is selected, Partek Flow will store new file paths with any symbolic links intact, making it easier to change where the links point. Otherwise, new paths are stored with symbolic links replaced by the directories to which they point, guaranteeing that Partek flow can uniquely identify each file and recognize when it already has information about that file. Changing the setting does not affect file paths already stored or the ability of Partek Flow to locate earlier files

Activity log retention

  • Number of months activity logs are kept for

Task queue and job processing

Figure 2. Editing the Task queue and job processing preferences

Start Internal worker at Partek Flow server startup

  • When enabled, an internal worker will be started upon server restart

Maximum running projects

  • Sets the maximum number of projects that will run simultaneously. Any tasks already running will be completed before this takes into effect

Adjust job nice value

  • Niceness value that is added to Partek Flow commands. Higher values are nicer. Set to 0 to disable

Show anonymous tasks on the queued tasks page

  • If Yes is selected, all users can view the tasks queued up on the server and tasks that are not shared with the user will appear as anonymous

Show warning when no workers are connected

  • If Yes is selected, a warning will be displayed when no workers are attached to the Partek Flow server

Email admins long running queued task

  • If Yes is selected, Partek Flow will email admins (Figure 3) if a running task has a remaining runtime longer than the specified days and adding more workers could speed up the task

Figure 3. Example of an email sent to Partek Flow administrators for predicted long runtimes

User quotas and limitations

Figure 4. Editing User quotas and limitations preferences

Only administrators can manage library files

  • If Yes is selected, only administrators can import and delete library files and regular users can only view library files

Only administrators can create system-wide attributes

  • If Yes is selected, only administrators can create system-wide attributes within projects

Upload file size limit

  • Size limit for files that can be uploaded using the My computer option

  • Setting this to 0 removes file size limit

Default disk quota (requires enterprise license)

  • Sets the default size of disk quota available for all users

  • Disk quotas for specific users can be set in the User management page

  • If Set as the quota for users having none is checked, disk quotas are retroactively set for all users currently without disk quotas

  • Selecting None means there are no disk quotas across all users

Actions at 80% of disk quota (requires enterprise license)

  • Specifies the actions when user reaches 80% of their disk quota

  • An email can be sent to the user and/or the administrators (Figure 5)

  • The user can also be prevented from importing additional samples and running tasks until they clear additional space

Figure 5. Example of an email sent to Partek Flow administrators about user quota

Actions at 100% of disk quota (requires enterprise license)

  • Specifies the actions when user reaches their disk quota

  • An email can be sent to the user and/or the administrators (similar to Figure 5)

  • The user can also be prevented from importing additional samples and running tasks until they clear additional space

Authentication settings

Figure 6. Configuring Authentication settings

Days for user to set password

  • If a user requests a password reset, this specifies amount of time the user has to reset their password

Use proxy server

  • Allows administrator to configure proxy settings for the Partek Flow server

  • Note that port number changes require a corresponding update to tomcat/conf/server.xml and a Partek Flow server restart

Allow users to override the default session timeout

  • If checked, this gives each user the ability to override the default session timeout with their own settings as specified in "My preferences"

Default session timeout

  • The amount of time, in minutes, before users are automatically logged out

  • This protects users in the event that they walk away from their computer

Require HTTPS for all pages

  • If checked, this requires HTTPS to load Partek Flow pages. Specify HTTPS port

Email settings

These settings allow Administrators to use the embedded email server within Partek Flow. Select the checkbox to configure mail server (Figure 7).

Figure 7. Configuring Email settings

Email users on transfer of project ownership

  • Administrators can configure whether email notifications are sent when project ownership is transferred. By selecting the relevant checkbox, the new or previous project owner can be notified.

Extra text to email to new users

  • If the Email users on creation checkbox is selected, new Partek Flow users will receive an email with a link to set their password within Partek Flow. The email will include this extra text, which may have URLs in it. This setting does not affect user accounts that come from LDAP, because these accounts use the password stored in LDAP, not in Partek Flow

General preferences

Figure 8. Editing General preferences

Data table decimal precision

  • Specifies the number of decimal places displayed

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

To edit preferences, select the drop-down menu for the specific section you would like to modify. Information about specific preferences can be obtained by hovering over the icon next to the option. Click the icon to start editing.