Loading and keeping bed files loaded with new sessions

[acl...@gmail.com]

Hi All,

I'm trying to get two custom bed files to auto-load when the IGV bat file is executed, and to maintain these two files after I create a new session. The two bed files are located in the same directory with the IGV bat file, and both can be loaded without any issues after IGV starts, so I'm confident it's not an issue with the file format.

I'm running Windows 10 and my bat file looks like this:

::Get the current batch file's short path

for %%x in (%0) do set BatchPath=%%~dpsx

for %%x in (%BatchPath%) do set BatchPath=%%~dpsx

jre1.8.0_131\bin\javaw  -Xmx10G -Dproduction=true -Djava.net.preferIPv4Stack=true -Dsun.java2d.noddraw=true -jar %BatchPath%lib\igv.jar -o C:\Users\<hidden>\igv\prefs.properties -o File1.bed -o File2.bed %*

I tried adding the text in red to options above, which didn't work. If I change the text to -o *.bed then one of the files loads, but the other never does. Is there a (better) way to get these two bed files to auto-load on startup? And once they are loaded, is there a way to get these two files to persist if I open a new session?

Thanks for any help. I'm stuck using Windows and am trying to make sense of modifying windows batch files. 

-Adam

[James Robinson]

The "-o" option is for preference files.   To load your data files just list them.   For example

jre1.8.0......   File1.bed  File2.bed -o C:\Users\<hidden>\igv\prefs.properties

The answer to your second question is no, the files are part of your current session and will be cleared when loading another session.

Command line arguments are documented here:  

http://software.broadinstitute.org/software/igv/startingIGV

[acl...@gmail.com]

Thanks for the quick reply James!

I'm seeing an interesting behavior with this method, where only the first file is loaded. The second file gets a pop-up window stating "Cannot find feature or locus: File2.bed" If I switch the order of files on the batch script, whichever is second will get this error message. Does IGV need some kind of delay between loading the two files in order for it to work properly?

Thanks again,

-Adam

[James Robinson]

What version if IGV are you using?

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[acl...@gmail.com]

2.4.10

On Tuesday, July 23, 2019 at 9:01:29 AM UTC-6, James Robinson wrote:

What version if IGV are you using?

On Tue, Jul 23, 2019 at 5:25 AM <acl...@gmail.com> wrote:

Thanks for the quick reply James!

I'm seeing an interesting behavior with this method, where only the first file is loaded. The second file gets a pop-up window stating "Cannot find feature or locus: File2.bed" If I switch the order of files on the batch script, whichever is second will get this error message. Does IGV need some kind of delay between loading the two files in order for it to work properly?

Thanks again,

-Adam

On Monday, July 22, 2019 at 5:26:27 PM UTC-6, James Robinson wrote:

The "-o" option is for preference files.   To load your data files just list them.   For example

jre1.8.0......   File1.bed  File2.bed -o C:\Users\<hidden>\igv\prefs.properties

The answer to your second question is no, the files are part of your current session and will be cleared when loading another session.

Command line arguments are documented here:  

http://software.broadinstitute.org/software/igv/startingIGV

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[James Robinson]

That's an old version, not supported anymore,  but if I recall correctly multiple files were separated by commas in that version.  So it would be  File1.bed,File2.bad,   or perhaps File1.bed%2CFile2.bed.

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[acl...@gmail.com]

Yeah, I need to update to a newer version of IGV. Commas are the solution I was looking for.

Thanks so much,

-Adam

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[Adam Clayton]

Resurrecting a bit of an old thread here. I've recently switched to using IGV on a mac running 2.19.7 and wondering how to get extra bed or bed.gz files to load at start. I tried adding them to the java_arguments file in the hidden .igv folder, but IGV refuses to start when I do this. Any other tips?

-Adam