Re: JBrowse bam - apache issue - suggested fixes not working

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Re: JBrowse bam - apache issue - suggested fixes not working

Mike Axtell
Hello again, I am following up on this help request sent last week, and also including the gmod-ajax listserv this time.

I've figured out that this is a VPN issue. The jbrowse I am currently running is behind an institutional firewall while the site is under development. If I use VPN to connect from outside my institution's network, I have the error, not matter what the mod_mime_magic status is. But when viewed from inside the firewall with no VPN, bam files are served fine so long as I've disabled the mime_magic module. Basically I think this is solved though if there is some trick to get it to show from a VPN connection, would love to hear it.

Thanks for your time,
Mike Axtell

On Fri, Nov 25, 2016 at 11:20 AM, Michael Axtell <[hidden email]> wrote:
Hello, I am having the "Error: Not a BAM file error" which is a known
issue of JBrowse when served by CentOS's default Apache configuration.
I followed the recommended methods to fix the error, but they failed
to fix the error. Details:

Commented out line “LoadModule mime_magic_module
modules/mod_mime_magic.so” in /etc/httpd/conf.modules.d/00-base.conf
.. restart apache .. module is indeed not loaded per http -M. But
JBrowse still has the error.

I also tried to add line “AddType application/octet-stream .bam .bami
.bai” to /etc/httpd/conf/httpd.conf both by itself and also within the
“<IfModule mime_module>” stanza where some other AddType directives
are located. This also failed to fix the issue.

Yes, the bam file I am testing is indeed valid at at the referenced location.

Here are the details of my server:

CentOS Linux release 7.2.1511 (Core)

Server version: Apache/2.4.6 (CentOS)
Server built:   Jul 18 2016 15:30:14

JBrowse version 1.21.1

tracks.conf snippet :

[tracks.SRR1013387_ca_bam]
urlTemplate = ../../alignments/SRR1013387_ca.bam
type = Alignments2


Thanks in advance for suggestions. Really do need to serve bam files
on my jbrowse.

Best,
Mike Axtell





--
Michael J. Axtell, Ph.D.
Professor of Biology
Penn State University
http://sites.psu.edu/axtell

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Re: JBrowse bam - apache issue - suggested fixes not working

Scott Cain
Hi Mike,

I had a very similar issue with WormBase's JBrowse instance, where WormBase runs on a reverse proxy and is blocked in a similar way.  The way I "fixed" it was to put all of our BAM and BigWig files on a webserver port outside of the proxy, whereas everything else (JBrowse proper and the GFF-based tracks) are served from inside the proxy.  It was a bit of a hassle diagnosing the problem (as you've already experienced), but since it's been set up, I've pretty much forgotten about it (I don't often have to add new binary file data).  This may be properly fixable in your case; I'm sure it varies.  Basically, you have to figure out how to properly transfer the range requests and responses threw the VPN.

Scott


On Mon, Nov 28, 2016 at 11:47 AM, Michael Axtell <[hidden email]> wrote:
Hello again, I am following up on this help request sent last week, and also including the gmod-ajax listserv this time.

I've figured out that this is a VPN issue. The jbrowse I am currently running is behind an institutional firewall while the site is under development. If I use VPN to connect from outside my institution's network, I have the error, not matter what the mod_mime_magic status is. But when viewed from inside the firewall with no VPN, bam files are served fine so long as I've disabled the mime_magic module. Basically I think this is solved though if there is some trick to get it to show from a VPN connection, would love to hear it.

Thanks for your time,
Mike Axtell

On Fri, Nov 25, 2016 at 11:20 AM, Michael Axtell <[hidden email]> wrote:
Hello, I am having the "Error: Not a BAM file error" which is a known
issue of JBrowse when served by CentOS's default Apache configuration.
I followed the recommended methods to fix the error, but they failed
to fix the error. Details:

Commented out line “LoadModule mime_magic_module
modules/mod_mime_magic.so” in /etc/httpd/conf.modules.d/00-base.conf
.. restart apache .. module is indeed not loaded per http -M. But
JBrowse still has the error.

I also tried to add line “AddType application/octet-stream .bam .bami
.bai” to /etc/httpd/conf/httpd.conf both by itself and also within the
“<IfModule mime_module>” stanza where some other AddType directives
are located. This also failed to fix the issue.

Yes, the bam file I am testing is indeed valid at at the referenced location.

Here are the details of my server:

CentOS Linux release 7.2.1511 (Core)

Server version: Apache/2.4.6 (CentOS)
Server built:   Jul 18 2016 15:30:14

JBrowse version 1.21.1

tracks.conf snippet :

[tracks.SRR1013387_ca_bam]
urlTemplate = ../../alignments/SRR1013387_ca.bam
type = Alignments2


Thanks in advance for suggestions. Really do need to serve bam files
on my jbrowse.

Best,
Mike Axtell





--
Michael J. Axtell, Ph.D.
Professor of Biology
Penn State University
http://sites.psu.edu/axtell



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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