My attempts to understand why a bigwig file cannot be loaded by UCSC through galaxy's display_application ended up with tcpdump... If anybody would like to help me understanding what's wrong (and different) here I would really appreciate it. If needed I can make the tcpdupms available for analysis with wireshark... [ TCP Stream for a bigWig served outside galaxy] [stream 1: after setting hgt.customText in hgTracks equal to a path with bigWig track definition] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:50:29 GMT Server: Apache/2.2.8 (Ubuntu) Last-Modified: Fri, 11 Jun 2010 13:37:28 GMT ETag: "7140-9f-488c13d753600" Accept-Ranges: bytes Content-Length: 159 Connection: close Content-Type: text/plain track type=bigWig name="therightone.bw" bigDataUrl=http://host001.instruments.ifom-ieo-campus.it/ga-data/galaxy_dist/database/f... db=hg18 [stream 2 ] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:50:29 GMT Server: Apache/2.2.8 (Ubuntu) Last-Modified: Thu, 10 Jun 2010 15:12:15 GMT ETag: "9f-42e5586-488ae729691c0" Accept-Ranges: bytes Content-Length: 70145414 Connection: close Content-Type: chemical/x-mopac-input [stream 3] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:50:36 GMT Server: Apache/2.2.8 (Ubuntu) Last-Modified: Thu, 10 Jun 2010 15:12:15 GMT ETag: "9f-42e5586-488ae729691c0" Accept-Ranges: bytes Content-Length: 70145414 Connection: close Content-Type: chemical/x-mopac-input [stream 4: I believe this is after I ask for a different region on chromosome] HTTP/1.1 206 Partial Content Date: Fri, 11 Jun 2010 13:50:37 GMT Server: Apache/2.2.8 (Ubuntu) Last-Modified: Thu, 10 Jun 2010 15:12:15 GMT ETag: "9f-42e5586-488ae729691c0" Accept-Ranges: bytes Content-Length: 9819526 Content-Range: bytes 60325888-70145413/70145414 Connection: close Content-Type: chemical/x-mopac-input %.:....3...@...=>.} [cut, note that the bigWig data are not from the beginning of file] [stream 5] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:50:40 GMT Server: Apache/2.2.8 (Ubuntu) Last-Modified: Thu, 10 Jun 2010 15:12:15 GMT ETag: "9f-42e5586-488ae729691c0" Accept-Ranges: bytes Content-Length: 70145414 Connection: close Content-Type: chemical/x-mopac-input [ TCP Stream for the same bigWig served within galaxy] [stream 1: after hgt.customText is set to the path served by galaxy] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:46:29 GMT Server: Apache/2.2.8 (Ubuntu) Last-Modified: Fri, 11 Jun 2010 13:36:56 GMT ETag: "713f-f7-488c13b8cee00" Accept-Ranges: bytes Content-Length: 247 Connection: close Content-Type: text/plain track type=bigWig name="wgEncodeYaleChIPseqRawDataRep2Helas3Pol2_fs.bw" bigDataUrl=http://host001.instruments.ifom-ieo-campus.it:8080/display_application/cac7b... db=hg18 [stream 2] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:46:29 GMT Server: PasteWSGIServer/0.5 Python/2.6.5 content-length: 70145414 content-type: chemical/x-mopac-input Set-Cookie: galaxysession=eb142648ac45b770ddabc752e2cd511e21664b5a654cabfbe79569d4ede184379f55c5dbc9000304; expires=Thu, 09-Sep-2010 15:46:29 GMT; Max-Age=7776000; Path=/; Version=1 Connection: close [stream 3: i get the error "http://host001.instruments.ifom-ieo-campus.it:8080/display_application/cac7b... is not a chromosome id r-tree index file" from the UCSC] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:46:29 GMT Server: PasteWSGIServer/0.5 Python/2.6.5 content-length: 70145414 content-type: chemical/x-mopac-input Set-Cookie: galaxysession=eb142648ac45b770233699f0ab65857e995c6e1b17d8e57d15b91a28b7b680af4cf210ffa8e6cc2a; expires=Thu, 09-Sep-2010 15:46:29 GMT; Max-Age=7776000; Path=/; Version=1 Connection: close &.......(......... [cut: note that bigWig data are served from the beginning, note that http headers are different] [stream 4: another attept to navigate on a different region of the chromosome] HTTP/1.1 200 OK Date: Fri, 11 Jun 2010 13:46:30 GMT Server: PasteWSGIServer/0.5 Python/2.6.5 content-length: 70145414 content-type: chemical/x-mopac-input Set-Cookie: galaxysession=eb142648ac45b7709206aaeef08ccecdd9d6070c5f8aed59d9ddd2079322251934ece94b298127df; expires=Thu, 09-Sep-2010 15:46:30 GMT; Max-Age=7776000; Path=/; Version=1 Connection: close &.......(...............$. [cut: again, the bigWig data are sent entirely from the beginning] /* 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 */