Hi Folks,
One issue with our staff working from home is using IGV. I wondered what would be involved/required to spin up a custom IGV singularity container runing a web server GUI for IGV and redirect an IGV web front end to OOD as an interactive app running on our SLURm cluster? From there remove, users could possibly upload BAM files, review, display them, etc in IGV.
I love the capabilities of the RStudio and gave a demo of OOD the other day to our research groups, they are so excited with the whole thing you are all doing. Great work is the feedback! This question came up by quite a few staff.
One of the ‘canned’ answers I always give when someone asks “can OOD do X” is: In general OOD can do X if a knowledgable and sophisticated user can do X on your systems using some combination of existing command line tools, scripts, and X windows. We’re not familiar with IGV (in fact I had to Google it to even find out what it was, just like with MetaShape from your earlier question), so the question I’d ask in return is how do your clients currently utilize / access it? What are the existing components that come with a standard installation of it?
We’ve successfully deployed MANY different types of apps within OnDemand, ranging from ones that traditionally would be accessed via a desktop or X11 connection (such as MATLAB or ANSYS) to ones that traditionally would require their own server and web stack (such as COMSOL or Jupyter). So I’m sure we can provide guidance on how to do virtually any other app.
Unfortunately, I am not an IGV user. Most use it on their workstations. I believe it is available on windows and Mac OSX and there is a version that embeds into web pages. There is an Rstidio and Jupiter notebook plugin that allows U to run it by calling methods bit that is not the use case our users are after.
Larger files. The issue is that we prevent upload and download of large files, so those (many) who work from home can grab an RDP desktop and use it on remote workstations. Using it remotely gives them access to all the files on the file server in a speedy fashion, but they are limited to two concurrent remote RDP (windows) connections per workstation which I am told is not enough to meet demand.
I will take a look at how OOD RStudio is configured and connects the interface to the OOD portal. Maybe I can figure out a solution.
IGV tool is heavily used in the bioinformatics, research and Molpath clinical space. I think it could be a welcome inclusion to the OOD inventory.
I suspect Melbourne University have IGV running via their implementation of OOD to their Spartan cluster, so as you mentioned, it is likely this could be made to work.
.Launching IGV
There are two ways; Launching IGV in your web browser or by downloading the binaries locally and running IGV from your machine.
Locally on the classroom machines booted in Linux
This downloads the IGV executable and tells the command line to launch it (via the java command).
wget http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.5.zip
unzip IGV_2.3.5.ziphttp://IGV_2.3.5.zip
cd IGV_2.3.5
java -Xmx2g -jar igv.jar
In a Web browser
Navigate a web browser to this page: http://www.broadinstitute.org/software/igv/download. You will need to register your email address to use this option!
Go ahead and click on the “Launch with 2 GB” option. This will download a “Java Web Start” file that you can launch by locating it on your Desktop and
double-clicking.
Yup, it’s definitely just an uncomplicated Java/X11 type app – we use it/I’ve installed it. Pretty basic. I have less experience with making my own apps for OOD than this app, but I suspect if you know how to do the former, the latter will be simple.
Installed IGV and it works fine. (THX) Users were wondering if the default could be resized. I cannot get the App to scale to fit more of the VNC window. Any idea what needs doing? Got an example? Tries bc_vnc_resolution and custom settings but no joy
Thx.
Browser screen dump. IGV takes only one third of the vnc window
Not sure if images get dropped in this forum but here’s the image.
Do you mind if we post links to this and other MCW OnDemand app repos in the documentation? We have a list of published apps from other sites we are building up in the dev version of the documentation here: https://osc.github.io/ood-documentation-test/develop/install-ihpc-apps.html that will be published sometime this or next week along with 1.7.
Our first attempt didn’t include a window manager. We’ve updated to include an Xfce window manager which enables resizing of the window. Most of this is taken directly from other OOD apps (Matlab, QGIS) as examples and adapted to IGV. For our cluster, we don’t have any desktop installed so this app makes use of Singularity to containerize Xfce.
You can install the container on your cluster with singularity pull shub://mcw-rcc/xfce-ood-desktop:latest. You’ll need to adjust the hard-coded location in template/script.sh.erb.
This is slightly more involved so your mileage may vary depending on the configuration of your cluster.
Yep, thought this approach may be necessary. And thx, I will give this a go.
Hey, Do you think this is a limitation with not being able to set IGV’s window size as a IGV parameter when it starts or with any app that starts in vnc without a window manager?
Not sure, as we haven’t tested another java app with this method. But I’d guess its an issue with any app without a window manager. We opted to use a variant of the default method. We’re working on a setting to start the window maximized as well. Although we’ve had no luck so far.
We’re using Xfce to support a windowed IGV. The window is then resizable. We based this on the OSC Matlab app. The specific configs are in the Git repo above. The file script.sh.erb syntax will depend on if you have Xfce installed in your host OS or if you need to use a container. In our cluster, we don’t have desktops on compute nodes, so we’ve containerized the commands that launch the window manager. Happy to help if you have more questions.
