Re: [galaxy-dev] Byte-range support for IGV ?
HI Geert ! I did well : <Location "/"> XSendFile on XSendFilePath / </Location> and <Location "/"> # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary </Location> But it dosen't fix it. I think that il is may be a problem of server byte-range accepting? Thanks Amine 2012/7/4 Geert Vandeweyer <geert.vandeweyer2@ua.ac.be>
Hi,
If I remember correctly, I solved this issue by enabling the xsendfile module in apache and setting galaxy to use the proxy for file downloading.
best regards,
Geert
On 07/04/2012 11:15 AM, Chebbi Mohamed Amine wrote:
HELLO !
I just updated our local galaxy instance and just wanted to try the new IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message :
"HTTP and FTP access to BAM files require byte-range support"
Has anyone encountred the same probleme?
Thanks in advances
Regards Amine
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweye...
On Jul 4, 2012, at 7:57 AM, Chebbi Mohamed Amine wrote:
HI Geert ! I did well :
<Location "/"> XSendFile on XSendFilePath / </Location>
and
<Location "/"> # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary </Location>
But it dosen't fix it.
Hi Amine, Did you also set use_sendfile = True in universe_wsgi.ini and restart the Galaxy server process? --nate
I think that il is may be a problem of server byte-range accepting?
Thanks Amine
2012/7/4 Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> Hi,
If I remember correctly, I solved this issue by enabling the xsendfile module in apache and setting galaxy to use the proxy for file downloading.
best regards,
Geert
On 07/04/2012 11:15 AM, Chebbi Mohamed Amine wrote:
HELLO !
I just updated our local galaxy instance and just wanted to try the new IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message :
"HTTP and FTP access to BAM files require byte-range support"
Has anyone encountred the same probleme?
Thanks in advances
Regards Amine
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
--
Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
HI Nate ! Thanks for your response. However, I have a little problem concerning the launch of IGV application from my local galaxy tool main. In fact to run IGV I have always to connect to my server machine where IGV is installed. So it is embarrassing, since that other users cannot display IGV in their own machines when they connect to my galaxy instance. Here above my xml file : <?xml version="1.0"?> <display id="igv_bam" version="1.0.0" name="display with IGV"> <command> java -Xmx1G -jar ~/tools/myTool/igv/igv.jar $input </command> <inputs> <param name="input" type="data" format="bam" label="input"/> </inputs> <outputs> <data name="output" /> </outputs> </display> Have I to modify it or maybe proceeding bu another way like setting a JNLP file ? Thanks Amine 2012/7/11 Nate Coraor <nate@bx.psu.edu>
On Jul 4, 2012, at 7:57 AM, Chebbi Mohamed Amine wrote:
HI Geert ! I did well :
<Location "/"> XSendFile on XSendFilePath / </Location>
and
<Location "/"> # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary </Location>
But it dosen't fix it.
Hi Amine,
Did you also set use_sendfile = True in universe_wsgi.ini and restart the Galaxy server process?
--nate
I think that il is may be a problem of server byte-range accepting?
Thanks Amine
2012/7/4 Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> Hi,
If I remember correctly, I solved this issue by enabling the xsendfile
module in apache and setting galaxy to use the proxy for file downloading.
best regards,
Geert
On 07/04/2012 11:15 AM, Chebbi Mohamed Amine wrote:
HELLO !
I just updated our local galaxy instance and just wanted to try the new
IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message :
"HTTP and FTP access to BAM files require byte-range support"
Has anyone encountred the same probleme?
Thanks in advances
Regards Amine
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
--
Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Chebbi Mohamed Amine -
Nate Coraor