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Sort sort an alignment file by start position. Usage: igvtools Ĭommand: version print the version number To see what options are available for the commandline IGVTools, just type igvtools at the prompt:

To allocate 20gb of memory, use: igvtools -memory 20g bedīy default, IGVTools uses 5gb of memory and the same temporary directory method as IGV.

index creates an index file for an input ascii alignment or feature file.sort sorts the input file by start position.count computes average alignment or feature density for over a specified window size across the genome.tile converts a sorted data input file to a binary tiled data (.tdf) file.IGVTools allows commandline utilities for working with ascii file formats. Input/output for IGV is menu-driven through the GUI. To allocate 20gb of memory, use: igv -memory 20g $USER is the login of the user running IGV. The igv command on Helix is wrapped to include two additional options:īy default, IGV uses 2gb of memory and uses either /lscratch/$SLURM_JOBID/igvtmp if -gres=lscratch: N is used in a batch job (where N is the number GB needed for scratch space, where This can override any properties IGV supports. -o or -preferences= A user preference properties file.-p or -port= Specify port IGV opens for port commands.-u or -genomeServerURL= Specify URL to genome registry file.-d or -dataServerURL= Specify URL to data registry file.NEW since 2.1.28: the -g option can specify a path to a.

You can locate the genomeId as the last entry in each line of the genome registry.

-g or -genome= Specify the genome by ID.

-b or -batch= Immediately run the supplied batch script after start up.

Salloc.exe: Relinquishing job allocation ~]$ Salloc.exe: Nodes cn3144 are ready for ~]$ module load IGV ~]$ igv -m ~]$ exit Salloc.exe: Waiting for resource configuration Salloc.exe: Granted job allocation 46116226 Salloc.exe: job 46116226 has been allocated resources When you have made your changes, click Apply and then OK. Then try scrolling one page at a time with the mouse or altering the number of lines to scroll with the mouse. In the Mouse Properties box, click the Wheel tab. Salloc.exe: job 46116226 queued and waiting for resources To access this window, open the Control Panel, choose Hardware and Sound, and then Mouse. Salloc.exe: Pending job allocation 46116226 Sample sinteractive -mem=8g -gres=lscratch:5 To manually change output settings (rotation, enabling/disabling outputs etc) use the KScreen KCM.Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.Īllocate an interactive session and run the program. System Settings -> Startup and Shutdown -> Service Manager, uncheck "KScreen 2"

Hence, if your X2Go Server machine is also used as a physical desktop machine, consider well, if it is OK to remove that package or not.įor X2Go we suggest disabling the KScreen KDED module in the user's profile, since X2Go handles resolution switches for you: The kscreen package handles hotplugging of display hardware. This, however, may have a negative effect on your X2Go server's plug'n'play capabilities. OpenStack Foundation, or the OpenStack community. On machines that act as an X2Go Server only, it may make sense to remove the kscreen package completely. Leostream is not affiliated with, endorsed or sponsored by the. Using two applications - kscreen and X2Go client applications' resizing features - that handle display resolution is not supported, as it can lead to many unexpected situations and race conditions. You might encounter an X2Go session trying to launch KDE and this KDE session not resizing properly to your client-side screen or session window size. This happens because of a package called kscreen.