.\" Manpage for vistrails
.\" Contact vistrails-dev@vistrails.org to correct errors or typos.
.TH man 1 "27 August 2015" "2.2.2" "vistrails man page"
.SH NAME
vistrails \- Scientific workflow and provenance management system
.SH SYNOPSIS
vistrails [-E] [-b] [-o DIR] [-p OUTPUTSETTINGS]
          [--parameters PARAMETERS] [--parameter-exploration]
          [--show-window] [--output-version-tree]
          [--output-pipeline-graph] [--graphs-as-pdf]
          [CONFIGURATION OPTIONS] [vistrail [vistrail ...]]
.SH DESCRIPTION
VisTrails is an open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, such as simulations, data analysis and visualization, very little is repeated---change is the norm. As an engineer or scientist generates and evaluates hypotheses about data under study, a series of different, albeit related, workflows are created while a workflow is adjusted in an interactive process. VisTrails was designed to manage these rapidly-evolving workflows.
.SH OPTIONS
.SS Arguments:
.TP
.B vistrail
Vistrail to open

.SS Options:
.TP
.B -h, --help
show this help message and exit
.TP
.B --version
show program's version and exit
.TP
.B -E, --no-execute
Do not execute specified workflows.
.TP
.B -b, --batch
Run vistrails in batch mode instead of interactive mode.
.TP
.B -o DIR, --output-directory DIR
.TP
.B -p OUTPUTSETTINGS, --output-settings OUTPUTSETTINGS
One or more comma-separated key=value parameters.
.TP
.B --parameters PARAMETERS
List of parameters to use when running workflow.
.TP
.B --parameter-exploration
Open and execute parameter exploration specified by the version argument after the .vt file.
.TP
.B --show-window
Show the main VisTrails window.
.TP
.B --output-version-tree
Output the version tree as an image.
.TP
.B --output-pipeline-graph
Output the workflow graph as an image.
  --graphs-as-pdf

.SS Paths:
.TP
.B -S DIR, --dot-vistrails DIR
The location to look for VisTrails user configurations and storage. Defaults to ~/.vistrails.
.TP
.B --subworkflows-dir DIR
The location where a user's local subworkflows are stored.
.TP
.B --data-dir DIR
The location that VisTrails uses as a default directory for data.
.TP
.B --package-dir DIR
The directory to look for VisTrails core packages (use userPackageDir for user-defined packages).
.TP
.B --user-package-dir DIR
The location for user-installed packages (defaults to ~/.vistrails/userpackages).
.TP
.B --file-dir DIR
The location that VisTrails uses as a default directory for specifying files.
.TP
.B --log-dir DIR
The path that indicates where log files should be stored.
.TP
.B --temporary-dir DIR
The directory to use for temporary files generated by VisTrails.

.SS Packages:
.TP
.B --enable-packages-silently
Do not prompt the user to enable packages, just do so automatically.
.TP
.B --no-enable-packages-silently
Inverse of --enable-packages-silently
.TP
.B --load-packages
Whether to load the packages enabled in the configuration file
.TP
.B --no-load-packages
Inverse of --load-packages
.TP
.B --install-bundles
Automatically try to install missing Python dependencies.
.TP
.B --no-install-bundles
Inverse of --install-bundles
.TP
.B --install-bundles-with-pip
Whether to try to use pip to install Python dependencies or use distribution support.
.TP
.B --no-install-bundles-with-pip
Inverse of --install-bundles-with-pip
.TP
.B --repository-local-path DIR
Path used to locate packages available to be installed.
.TP
.B --repository-httpurl URL
URL used to locate packages available to be installed.

.SS Jobs:
.TP
.B --job-check-interval JOBCHECKINTERVAL
How often to check for jobs (in seconds, default=600).
.TP
.B --job-autorun JOBAUTORUN
Run jobs automatically when they finish.
.TP
.B --job-list
List running workflows.
.TP
.B --job-info
List jobs in running workflow

.SS Thumbnails:
.TP
.B --thumbs-auto-save
Whether to save thumbnails of results when executing VisTrails.
.TP
.B --no-thumbs-auto-save
Inverse of --thumbs-auto-save
.TP
.B --thumbs-mouse-hover
Whether to show thumbnails when hovering over a version in the version tree.
.TP
.B --no-thumbs-mouse-hover
Inverse of --thumbs-mouse-hover
.TP
.B --thumbs-tags-only
If True, only stores thumbnails for tagged versions.  Otherwise, stores thumbnails for all versions.
.TP
.B --no-thumbs-tags-only
Inverse of --thumbs-tags-only
.TP
.B --thumbs-cache-dir DIR
The directory to be used to cache thumbnails.
.TP
.B --thumbs-cache-size THUMBS.CACHESIZE
The size (in MB) of the thumbnail cache.

.SS Database:
.TP
.B --host URL
The hostname for the database to load the vistrail from.
.TP
.B --port PORT
The port for the database to load the vistrail from.
.TP
.B --db DB
The name for the database to load the vistrail from.
.TP
.B --user USER
The username for the database to load the vistrail from.

.SS Startup:
.TP
.B --maximize-windows
Whether the VisTrails windows should take up the entire screen space.
.TP
.B --no-maximize-windows
Inverse of --maximize-windows
.TP
.B --multi-heads
Whether or not to use multiple screens for VisTrails windows.
.TP
.B --no-multi-heads
Inverse of --multi-heads
.TP
.B --show-splash
Whether the VisTrails splash screen should be shown on startup.
.TP
.B --hide-splash
Inverse of --show-splash

.SS Server:
.TP
.B --rpc-server RPCSERVER
Hostname or ip address where this xml rpc server will work.
.TP
.B --rpc-port RPCPORT
Port where this xml rpc server will work.
.TP
.B --rpc-log-file DIR
Log file for XML RPC server.
.TP
.B --rpc-instances RPCINSTANCES
Number of other instances that vistrails should start.
.TP
.B --multithread
Server will start a thread for each request.
.TP
.B --rpc-config DIR
Config file for server connection options.

.SS Web Sharing:
.TP
.B --web-repository-url URL
The URL of the web repository that should be attached to VisTrails (e.g. www.crowdlabs.org).
.TP
.B --web-repository-user WEBREPOSITORYUSER
The default username for logging into a VisTrails web repository like crowdLabs.

.SS Upgrades:
.TP
.B --upgrades
Whether to upgrade old workflows so they work with newer packages.
.TP
.B --no-upgrades
Inverse of --upgrades
.TP
.B --migrate-tags
Whether or not the tag on a workflow that was upgraded should be moved to point to the upgraded version.
.TP
.B --no-migrate-tags
Inverse of --migrate-tags
.TP
.B --hide-upgrades
Don't show the "upgrade" nodes in the version tree.
.TP
.B --no-hide-upgrades
Inverse of --hide-upgrades
.TP
.B --upgrade-delay
Persist upgrade only after other changes.
.TP
.B --no-upgrade-delay
Inverse of --upgrade-delay
.TP
.B --upgrade-module-fail-prompt
Whether to alert the user when an upgrade may fail when upgrading a subworkflow.
.TP
.B --no-upgrade-module-fail-prompt
Inverse of --upgrade-module-fail-prompt

.SS Interface:
.TP
.B --auto-connect
Try to automatically connect a newly dragged in module to the rest of the workflow.
.TP
.B --no-auto-connect
Inverse of --auto-connect
.TP
.B --detach-history-view
Show the version tree in a separate window.
.TP
.B --no-detach-history-view
Inverse of --detach-history-view
.TP
.B --show-connection-errors
Alert the user if the value along a connection doesn't match connection types.
.TP
.B --hide-connection-errors
Inverse of --show-connection-errors
.TP
.B --show-variant-errors
Alert the user if the value along a connection coming from a Variant output doesn't match the input port.
.TP
.B --hide-variant-errors
Inverse of --show-variant-errors
.TP
.B --show-debug-popups
Always show the debug popups or only if there is a modal widget.
.TP
.B --hide-debug-popups
Inverse of --show-debug-popups
.TP
.B --show-scrollbars
Whether VisTrails should show scrollbars on the version tree and workflow canvases.
.TP
.B --hide-scrollbars
Inverse of --show-scrollbars
.TP
.B --show-inline-parameter-widgets
Show editable parameters inside modules
.TP
.B --hide-inline-parameter-widgets
Inverse of --show-inline-parameter-widgets
.TP
.B --shell-font-face SHELL.FONTFACE
The font to be used for the VisTrails console.
.TP
.B --shell-font-size SHELL.FONTSIZE
The font size used for the VisTrails console.
.TP
.B --max-recent-vistrails MAXRECENTVISTRAILS
How many recently opened vistrails should be stored for "Open Recent" access.
.TP
.B --view-on-load VIEWONLOAD
Whether to show pipeline or history view when opening vistrail Can be either appropriate/pipeline/history
.TP
.B --enable-custom-version-colors
.TP
.B --no-enable-custom-version-colors
Inverse of --enable-custom-version-colors
.TP
.B --fixed-custom-version-color-saturation
.TP
.B --no-fixed-custom-version-color-saturation
Inverse of --fixed-custom-version-color-saturation

.SS General:
.TP
.B --auto-save
Automatically save vistrails to allow recovery from crashes, etc.
.TP
.B --no-auto-save
Inverse of --auto-save
.TP
.B --db-default
Use a database as the default storage location for vistrails entities.
.TP
.B --no-db-default
Inverse of --db-default
.TP
.B --cache
Cache previous results so they may be used in future computations.
.TP
.B --no-cache
Inverse of --cache
.TP
.B --stop-on-error
Whether or not VisTrails stops executing the rest of the workflow if it encounters an error in one module.
.TP
.B --no-stop-on-error
Inverse of --stop-on-error
.TP
.B --execution-log
Track execution provenance when running workflows.
.TP
.B --no-execution-log
Inverse of --execution-log
.TP
.B --error-log
Write errors to a log file.
.TP
.B --no-error-log
Inverse of --error-log
.TP
.B --default-file-type DEFAULTFILETYPE
Defaults to .vt but could be .xml.
.TP
.B -v DEBUGLEVEL, --debug-level DEBUGLEVEL
How much information VisTrails should alert the user about (0: Critical errors only, 1: Critical errors and warnings, 2: Critical errors, warnings, and log messages).
.TP
.B --handler-dont-ask HANDLERDONTASK
Do not ask about extension handling at startup (Linux only).

.SS Advanced:
.TP
.B --single-instance
Whether or not VisTrails should only allow one instance to be running.
.TP
.B --no-single-instance
Inverse of --single-instance
.TP
.B --static-registry DIR
If specified, VisTrails uses an XML file defining the VisTrails module registry to load modules instead of from the packages directly.
.SH AUTHOR
VisTrails is currently developed at New York University.
.SH SEE ALSO
Homepage: http://www.vistrails.org/