Hi Manuel, Thanks! I've already taken the easy route and switched to nginx, but if I need to switch back to Apache I'll build from source as you've described below. Best, -Kip On Mon, Oct 17, 2011 at 1:14 PM, Manuel Kohler <manuel.kohler@bsse.ethz.ch>wrote:
Hi Kip, I had exactly the same problem you had, but I finally got it working. So there is some hope :-) I am running Galaxy behind an Apache with RHEL 6.1. The default Apache provided by RH was 2.2.15 which gave me exactly the same error. So I upgraded to 2.2.21 using the src rpms from Fedora16 which did not help. But with being on 2.2.21 I patched the Apache server with the following file which finally solved the byte range issue:
http://svn.apache.org/viewvc?view=revision&revision=1177080
The bug is described here: https://issues.apache.org/bugzilla/show_bug.cgi?id=51878 Galt Barber from UCSC Genome Browser already commented on this.
To be able to build Apache on your own you can do something like this:
# rpm -i /root/httpd-2.2.21-1.fc16.src.rpm # cd /root/rpmbuild/SPECS # rpmbuild -ba httpd.spec
We edited the httpd.spec file and removed the dependency to systemd-units so the following should work then.
# rpm -U /root/rpmbuild/RPMS/x86_64/httpd-2.2.21-1.el6.x86_64.rpm /root/rpmbuild/RPMS/x86_64/httpd-devel-2.2.21-1.el6.x86_64.rpm /root/rpmbuild/RPMS/x86_64/httpd-tools-2.2.21-1.el6.x86_64.rpm /root/rpmbuild/RPMS/x86_64/mod_ssl-2.2.21-1.el6.x86_64.rpm /root/rpmbuild/RPMS/noarch/httpd-manual-2.2.21-1.el6.noarch.rpm
It might be helpful to work together with a Sysadmin.
Cheers Manuel
-- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Mattenstr. 26 (1058), CH-4058 Basel, +41 61 387 3132 Switzerland
Hi Brad,
They're binary BAM files. I followed the section below, but perhaps I missed something. Thanks for the clarification on the Paste server, and I think I'll try nginx next if I can't get forwarding through Apache to work.
Cheers,
-Kip
On Thu, Oct 13, 2011 at 1:17 PM, Brad Chapman <chapmanb@50mail.com <mailto:chapmanb@50mail.com>> wrote:
Kip; Are these binary BAM or BigWig type files you are having trouble displaying at UCSC? I don't believe the Paste server has support for
On 14. October 2011 6:56 PM, Kip Bodi wrote: the
byte-range requests that UCSC needs, and you need to send files
through
the proxy server. I've done this with nginx so don't have direct
Apache
experience here, but the 'Sending files using Apache' section here should get it working:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
Brad
> Perhaps this is a distribution issue. For those who have gotten the "Display > at UCSC" link to work on a local server or workstation, what linux > distribution and version did you use? Has anyone used this successfully with > Red Hat Enterprise Linux 6.1? > > Best, > > -Kip > > On Fri, Oct 7, 2011 at 6:28 PM, Bodi, Kip <Kip.Bodi@tufts.edu <mailto:Kip.Bodi@tufts.edu>> wrote: > > > Hi all, > > > > I have a local galaxy instance, proxied by Apache, and am trying to get the > > 'display at UCSC' link to work. I've followed all of the instructions and am > > nearly there, but now I'm getting this response from UCSC when it tries to > > load the track: > > > > "Byte-range request was ignored by server. Expected Partial Content 206." > > etc. > > > > I think the error is because the PasteWSGIServer isn't allowing byte-range > > requests. When I look at the header, "Accept-Ranges: bytes" is not present: > > [galaxy@galaxy galaxy_dist]$ curl --head localhost > > HTTP/1.1 200 OK > > Date: Fri, 07 Oct 2011 22:23:49 GMT > > Server: PasteWSGIServer/0.5 Python/2.6.6 > > content-type: text/html; charset=UTF-8 > > Set-Cookie: > >
galaxysession=c6ca0ddb55be603a4e98b4f13a4db8bfb8635f0aa576697114d40b13a8355efe2cf7a075ef81d769;
> > expires=Thu, 05-Jan-2012 17:23:49 GMT; Max-Age=7776000; Path=/; Version=1 > > Vary: Accept-Encoding > > Connection: close > > > > Whereas on another server, "Accept-Ranges: bytes" appears in the header: > > [galaxy@galaxy galaxy_dist]$ curl --head apollo.med.tufts.edu <http://apollo.med.tufts.edu><; > > http://apollo.med.tufts.edu> > > HTTP/1.1 403 Forbidden > > Date: Fri, 07 Oct 2011 22:22:42 GMT > > Server: Apache/2.2.21 (Fedora) > > Accept-Ranges: bytes > > Content-Length: 4609 > > Connection: close > > Content-Type: text/html; charset=UTF-8 > > > > I'm running RHEL6 with the latest version of galaxy-dist. I've tried > > manually enabling 'accept-ranges' but haven't had any luck. Any suggestions? > > Can I enable it somehow in universe_wsgi.ini? > > > > Best, > > > > -Kip
-- Kip Lord Bodi Jr. Tufts University School of Medicine 136 Harrison Avenue, South Cove 502 Boston, MA 02118 617-636-3763 <tel:617-636-3763> kip.bodi@tufts.edu <mailto:kip.bodi@tufts.edu> www.tucf.org <http://www.tucf.org> | genomics.med.tufts.edu <http://genomics.med.tufts.edu>
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-- Kip Lord Bodi Jr. Tufts University School of Medicine 136 Harrison Avenue, South Cove 502 Boston, MA 02118 617-636-3763 kip.bodi@tufts.edu www.tucf.org | genomics.med.tufts.edu