Apollo cannot start

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Apollo cannot start

Praveen Kumar Raj Kumar
Hi,
   I installed apollo(Apollo_windows_with_jre) in 64 bit windows 7.  I did not have any installation problem. When I launch it says "JVM could not be started. The main method can be thrown an exception ". Please let me know of this.
Thank you,

--
Praveen K. Raj Kumar,
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Re: Apollo cannot start

Ed Lee
Hi Praveen,

You might want to try running the Apollo batch file if the installer
isn't working.  You can get the batch file at:

http://apollo.berkeleybop.org/current/apollo_batch.zip

See the Windows download instructions on setting up the batch file:

http://apollo.berkeleybop.org/current/install.html#windows

Cheers,
Ed

On Mon, 29 Nov 2010, Praveen Kumar Raj Kumar wrote:

> Hi,   I installed apollo(Apollo_windows_with_jre) in 64 bit windows 7.  I
> did not have any installation problem. When I launch it says "JVM could not
> be started. The main method can be thrown an exception ". Please let me know
> of this.
> Thank you,
>
> --
> Praveen K. Raj Kumar,
>
>
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GFF3 support

Lukas A. Mueller
Hi Ed,

I'm working with Apollo and am coming across some weirdness, where I'm not sure if it is Apollo or me, or something else, such as the datasets I'm using.

I have a pretty large file (chromosome-sized chunks) of tomato annotation data in gff3 format. I load it into Apollo and the tracks show up on both strands. When I zoom in, at some point, all the gene models seem to jump to the minus strand. And that's a little odd. Anything like that been seen before?

The chromosome sequence is about 80MB and has a few thousand gene models on it, and obviously I would like to load support data (alignments of ESTs, and 454 data, the latter obviously crash Apollo completely).

I admit I futzed with the config file somewhere buried in the Apollo.app folder (using it on MacOSX). I changed the startup memory parameter for Java (at least I believe I did) to 2GB.

Any help appreciated. I can also give you the actual datasets I'm using, but probably I should not send those to the list...

cheers
Lukas



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Re: GFF3 support

Lukas A. Mueller
Hi Ed,

Oops, I think I solved the problem... The one strand was just scrolled into oblivion...

sorry for the hassle - but maybe that scrolling pane behavior on zoom-in could be changed??

cheers
Lukas

On Nov 29, 2010, at 11:56 PM, Lukas Mueller wrote:

> Hi Ed,
>
> I'm working with Apollo and am coming across some weirdness, where I'm not sure if it is Apollo or me, or something else, such as the datasets I'm using.
>
> I have a pretty large file (chromosome-sized chunks) of tomato annotation data in gff3 format. I load it into Apollo and the tracks show up on both strands. When I zoom in, at some point, all the gene models seem to jump to the minus strand. And that's a little odd. Anything like that been seen before?
>
> The chromosome sequence is about 80MB and has a few thousand gene models on it, and obviously I would like to load support data (alignments of ESTs, and 454 data, the latter obviously crash Apollo completely).
>
> I admit I futzed with the config file somewhere buried in the Apollo.app folder (using it on MacOSX). I changed the startup memory parameter for Java (at least I believe I did) to 2GB.
>
> Any help appreciated. I can also give you the actual datasets I'm using, but probably I should not send those to the list...
>
> cheers
> Lukas
>
>
>