Question: Portable genome browser
0
gravatar for Lee Katz
3.5 years ago by
Lee Katz3.0k
Atlanta, GA
Lee Katz3.0k wrote:

Hi, does anyone have a method for sending a genome browser over email? I have a genbank file of interest and would like to share it with my colleagues who do not use the command line or many bioinformatics tools. Additionally, we do not have a centralized genome browser at work. I think it would be fantastic if I could, for example, package up a JBrowse instance and email it to someone to open in their web browser.

Edit some possible solutions would be

  • A packaged, self-extracting tool
  • A set of HTML/JS files that can open in a web browser
  • A URL to a public website where they can host a private session for my custom tracks and assemblies.
ADD COMMENTlink modified 3.3 years ago by cmdcolin1.3k • written 3.5 years ago by Lee Katz3.0k

can you share it using UCSC custom tracks ? https://genome.ucsc.edu/goldenpath/help/hgSessionHelp.html#Share

ADD REPLYlink written 3.5 years ago by Pierre Lindenbaum124k

I've never really used UCSC much but I'll try it. My first impression so far is that it's not immediately obvious how to change the assembly from HG38 to my own bacterial one.

ADD REPLYlink written 3.5 years ago by Lee Katz3.0k

Not sure what "sending a genome browser" you are referring to entails (I assume you mean a custom genome?). IGV also should be able to use genbank format files, if you made a custom genome in it.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax75k

My colleagues do not have IGV on their computers or anything similar. I think I'd like some self-extracting genome browser or something to work in a web browser when opened as an attachment. Another option is to have a hyperlink to some public website like UCSC or Galaxy that allows custom and private sessions.

ADD REPLYlink written 3.5 years ago by Lee Katz3.0k

IGV is a single file download (there is even a web start but that may not work with custom genomes). I suppose you could download IGV and set things up the way you like them, zip the folder back up and send it to them. If they can't handle something as simple as unzipping and running one jar file then I wish you luck!

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax75k

I love IGV and use it; however it is not immediately clear how I could save a session complete with features and a reference assembly such that my colleagues could open the session from their email. I am also not clear how I'd zip all of IGV and send it over email when my size limit is 20MB and the current package is 750MB.

ADD REPLYlink written 3.5 years ago by Lee Katz3.0k

Can you temporarily host the archive on a web location for them to download? Technically you would be redistributing IGV so that may be against the use license (but I will assume this is a small number of people in a private collaboration). It may also be possible to remove the default human genome components since you don't need those (further reducing the size of the download).

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax75k

No, I am not allowed to host a website at my work unfortunately, and I am ethically disinclined to redistribute IGV. The files have to go through email.

ADD REPLYlink written 3.5 years ago by Lee Katz3.0k
1

It is possible to save a session and share with a colleague. Instructions are here. Your colleagues will need to download and install IGV. Just in case genoverse does not work.

ADD REPLYlink written 3.5 years ago by genomax75k

Then Genoverse mentioned below may be a lean option. Looks like a 5 Mb download.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax75k
2
gravatar for Jean-Karim Heriche
3.5 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

Have a look at Genoverse.

Genoverse is a portable, customizable, back-end independent JavaScript and HTML5 based genome browser which allows the user to explore data interactively.

ADD COMMENTlink written 3.5 years ago by Jean-Karim Heriche21k

This is beautiful. I will try it out.

ADD REPLYlink written 3.5 years ago by Lee Katz3.0k

Unfortunately, running this and probably any other JS-based browser locally will trigger cross-site errors, as I have learned from Genoverse this morning. I thought that a JS-based client would be the optimal solution; however, there is a fundamental security obstacle.

ADD REPLYlink written 3.5 years ago by Lee Katz3.0k

Have you considered packaging it (or maybe something else) with a web server in a virtual machine ?

ADD REPLYlink written 3.5 years ago by Jean-Karim Heriche21k

@Lee needs to be able to send this via email.

ADD REPLYlink written 3.5 years ago by genomax75k

I appreciate the idea @Jean, but @genomax2 is right that I would like to send something interactive over email. I can package and prepare something, but it needs to be ready to go when the recipient opens it from email.

ADD REPLYlink written 3.5 years ago by Lee Katz3.0k

I think you need to go back and revisit the IGV sessions idea that I had posted above. People would need to install IGV on their local machines. A thought.

ADD REPLYlink written 3.5 years ago by genomax75k
1
gravatar for cmdcolin
3.3 years ago by
cmdcolin1.3k
United States
cmdcolin1.3k wrote:

JBrowse has recently been released with a "desktop" mode, which is a simple exe file that you can download and run and get the jbrowse functionality without running a webserver.

enter image description here

You can have your colleagues download the OSX or Windows zip files for desktop jbrowse from the releases page http://jbrowse.org/jbrowse-1-12-1/

Then you can send them a "data directory" with the data that you have prepared for them (e.g. you could run the normal jbrowse processes like prepare-refseqs.pl, flatfile-to-json.pl, etc) or just send them files (fasta, gff, etc) that they can open.

ADD COMMENTlink written 3.3 years ago by cmdcolin1.3k

This would be in contrast to running jbrowse instances on the web, where sharing URLs to jbrowse also works well. The desktop mode is offered as an alternative! Feel free to make suggestions on github for jbrowse if interested. The desktop mode was announced in the recent genome biology paper

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by cmdcolin1.3k

looks like that link no longer works

ADD REPLYlink written 6 months ago by steve2.4k

New releases are available on this page.

ADD REPLYlink written 6 months ago by genomax75k
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