Genomics

IGV, the alignmentin front of you

The Integrative Genomics Viewer, on an Ubuntu desktop of your own.Tracks, coverage and annotations over a reference, on the volume.

IGV 2.18.54 cores · 8 GBOpens in a browser tab

hub://igv

$ dxflow workflow create --identity igv hub://igv --start --link

01Pick a machinecores, memory and a rate per hour

02Create the workflowpulled from the hub, once

03Run it, then stopstopped when the work is done

The application

Look at it,before you trust it

Numbers hide things that one look at the pileup makes obvious.

Reads over a reference

BAM and CRAM tracks, drawn against the reference underneath.

Down to the base

Search a gene or a coordinate, and zoom until the bases show.

Tracks, stacked

Coverage, variants and annotations in the one window at once.

How you run it

Every defaultis one override away

The session reads its settings from the environment, so you set them on the start line.

VNC_PASSWORDWhat the tab asks for. It ships as dxflow, and everyone reading this knows that.

PANEL and TASKBARBoth hidden, so the track view has the whole screen. Show either one to get the desktop back.

AUDIOOff here, since there is nothing to hear. Turn it on and the desktop sound follows the picture.

start it your way

$ dxflow workflow start igv --override env.app.VNC_PASSWORD=something-long

$ dxflow workflow start igv --override env.app.TASKBAR=show --link

The session

The viewerfills the screen

Streamed to your browser, with IGV already maximized.

6082Browserin the tab, at /vnc.html

5901VNCin a native client

/volumeStorageyour files, kept between runs

Open it from anywhereStart with --link and the session comes back on an HTTPS address.

Set a password firstVNC_PASSWORD defaults to dxflow, and everyone can read this page.

Good to know

A desktop app,in a headless category

The rest of genomics here runs as a job. IGV is the one you sit in front of.

Genomes arrive on demand

A reference is fetched the first time you pick it, so the session wants a way out. A local genome or FASTA off the volume works without one.

Built on Ubuntu

Void packages none of the genomics stack, so this one sits on the Ubuntu desktop instead.

Sessions belong on the volume

Tracks, indexes and saved sessions under /volume come back next time. Anything else does not.

The image

Pulled once,then it stays

IGV arrives as one image. This is what comes down the first time, and what the disk should have free for it.

677Mamd64compressed, the way the registry counts it

665Marm64compressed, the way the registry counts it

20GOn diskunpacked, with room to work beside it

ghcr.io/dxflow-ai/igv:latestPublished from the hub, pulled on the first start and kept for the ones after it.

Either architectureamd64 and arm64 are both published, and the machine pulls the one it runs.

What it asks for

What it wants,and what it needs

The definition asks for 4 cores and 8 GB. The image comes up on less than that, and a start given --fit trims the ask to whatever the machine actually has.

4 cores · 8 GBAsks forwhat the definition writes down

2 cores · 4 GBRuns onthe least the image comes up on

Not neededGPUit works on the cores alone

The ask is not the floorThe definition writes down what suits the work. The image itself starts on less, which is what the second figure is.

--fit caps it to the hostA start given --fit trims each step to what the machine actually has, for that start alone. The definition is never rewritten.

Machines that fit it

IGV asks for 4 cores and 8 GB. Cheapest first.

E2 Standard-4

$0.168/ hour4 cores · 16 GBStart this machine

T4g XLarge

$0.168/ hour4 cores · 16 GBStart this machine

C7g XLarge

$0.181/ hour4 cores · 8 GBStart this machine

Run IGV on your own machinePick a machine that meets it, and it opens about a minute after you ask.

Start IGV Browse workflows