Hi again... I still have problems in visualizing on external UCSC sites using the display_application... I've implemented bigWig data format, and it works (not really the sniffer but who cares at the moment?).... What is important is that the display_applications gives me a link to the genome browser that is correct:

http://host001.instruments.ifom-ieo-campus.it:8080/display_application/cac7b9b902f807f2/ucsc_bigwig/campus

which points to

http://genome.ifom-ieo-campus.it/cgi-bin/hgTracks?db=hg18&hgt.customText=http%3A%2F%2Fhost001.instruments.ifom-ieo-campus.it%3A8080%2Fdisplay_application%2Fcac7b9b902f807f2%2Fucsc_bigwig%2Fcampus%2F090e9746a4403c88%2Fparam%2Ftrack

which has this link in hgt.customText

http://host001.instruments.ifom-ieo-campus.it:8080/display_application/cac7b9b902f807f2/ucsc_bigwig/campus/090e9746a4403c88/param/track

which says

track type=bigWig name="wgEncodeYaleChIPseqRawDataRep2Helas3Pol2_fs.bw" bigDataUrl=http://host001.instruments.ifom-ieo-campus.it:8080/display_application/cac7b9b902f807f2/ucsc_bigwig/campus/090e9746a4403c88/data/galaxy_cac7b9b902f807f2.bw db=hg18

Everything is correct, apparently...
Needles to say, the bigWig file is fully operational meaning that:
1- if I download the bigDataUrl to another machine and show that file through another apache, the genome browser can read it
2- the original file can be seen and loaded.

BTW, the genome browser complains:

http://host001.instruments.ifom-ieo-campus.it:8080/display_application/cac7b9b902f807f2/ucsc_bigwig/campus/090e9746a4403c88/data/galaxy_cac7b9b902f807f2.bw is not a chromosome id r-tree index file

That probably means that there's something between the genome browser and the bigWig file (galaxy?) which passes wrong data/headers or possibly is passing something *before* the actual bigWig data stream...
As I have issues with BAM files too, I believe the cause may be the same... 

Any help/hint/debug strategy is really appreciated!

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it
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