Is galaxy returning an html page rather than the desired bam file?
Are you using an nginx or apache proxy server to your galaxy server?
I think that may be required, in order to view BAM files in IGV directly from
Galaxy.
JJ
On 11/29/13, 11:00 AM, galaxy-user-requ...@lists.bx.psu.edu wrote:
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Today's Topics:
1. Problem loading BAM into IGV browser - invalid GZIP header
error message (Vosberg, Sebastian)
2. Re: Problem loading BAM into IGV browser - invalid GZIP
header error message (Jim Robinson)
----------------------------------------------------------------------
Message: 1
Date: Fri, 29 Nov 2013 11:04:48 +0100
From: "Vosberg, Sebastian" <sebastian.vosb...@helmholtz-muenchen.de>
To: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] Problem loading BAM into IGV browser - invalid
GZIP header error message
Message-ID:
<20854588711e4a489a3ad70c9ba5548a01ae291c4...@xch11.scidom.de>
Content-Type: text/plain; charset="utf-8"
Dear all,
sometimes I encouter a problem trying to load BAM files directly from Galaxy into the IGV
browser. First I am starting the IGV browser locally, then clicking on the appropriate
BAM file and on "display with IGV _local_" in Galaxy. In most cases it works,
but for some reasons not with specific files. The error message says
"Error loading http://_URL-to-file_/galaxy_example.bam: An error occured while
accessing http://_URL-to-file_/galaxy_example.bam
Invalid GZIP header"
What does it mean? And why am I able to download the BAM file and load it from
HDD into the IGV?
The problem comes with all BAM files of one sample cohort, but not with another
(but same sample design and workflow used). Rerunning the workflow doesn't
help...
I would be very thankful for every kind of help!
Best,
Sebastian
Helmholtz Zentrum M?nchen
Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
Ingolst?dter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
Gesch?ftsf?hrer: Prof. Dr. G?nther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen
Registergericht: Amtsgericht M?nchen HRB 6466
USt-IdNr: DE 129521671
------------------------------
Message: 2
Date: Fri, 29 Nov 2013 09:42:42 -0500
From: Jim Robinson <jrobi...@broadinstitute.org>
To: "Vosberg, Sebastian" <sebastian.vosb...@helmholtz-muenchen.de>,
"galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] Problem loading BAM into IGV browser -
invalid GZIP header error message
Message-ID: <5298a7e2.7000...@broadinstitute.org>
Content-Type: text/plain; charset=UTF-8; format=flowed
Hi Sebastian,
Is it possible to share an example bam that exhibits this problem on a
Galaxy server I can reach? Also, which version of IGV are you using
(select Help > About... to see the version).
-- Jim
Dear all,
sometimes I encouter a problem trying to load BAM files directly from Galaxy into the IGV
browser. First I am starting the IGV browser locally, then clicking on the appropriate
BAM file and on "display with IGV _local_" in Galaxy. In most cases it works,
but for some reasons not with specific files. The error message says
"Error loading http://_URL-to-file_/galaxy_example.bam: An error occured while
accessing http://_URL-to-file_/galaxy_example.bam
Invalid GZIP header"
What does it mean? And why am I able to download the BAM file and load it from
HDD into the IGV?
The problem comes with all BAM files of one sample cohort, but not with another
(but same sample design and workflow used). Rerunning the workflow doesn't
help...
I would be very thankful for every kind of help!
Best,
Sebastian
Helmholtz Zentrum M?nchen
Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
Ingolst?dter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
Gesch?ftsf?hrer: Prof. Dr. G?nther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen
Registergericht: Amtsgericht M?nchen HRB 6466
USt-IdNr: DE 129521671
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End of galaxy-user Digest, Vol 89, Issue 25
*******************************************
--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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