Hey,

after clicking on the appropriate link in the Galaxy history, a new tab 
(without any further content) opens. It is loading until the IGV has completed 
to import the BAM, that's how it always used to work.

IGV is currently the Version 2.3.12, but also other versions are in use. I am 
using a VPN tunnel connection to access the Galaxy system (not Galaxy main).

As I said, in most cases (80-90%) it works without any problems to load BAM 
files into IGV. Unfortunately not for every single sample....

Thanks again!

Best,
Sebastian
-----------------------------------------------
________________________________________
From: Jim Johnson [johns...@umn.edu]
Sent: Friday, November 29, 2013 10:35 PM
To: Vosberg, Sebastian; jrobi...@broadinstitute.org
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: Problem loading BAM into IGV browser - invalid GZIP header error 
message

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:
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>     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
>>
>> ___________________________________________________________
>> 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:
>>
>>     http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>     http://lists.bx.psu.edu/
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>> To search Galaxy mailing lists use the unified search at:
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>>     http://galaxyproject.org/search/mailinglists/
>
>
> ------------------------------
>
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> End of galaxy-user Digest, Vol 89, Issue 25
> *******************************************


--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

Helmholtz Zentrum München
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
Ingolstädter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe
Geschäftsführer: Prof. Dr. Günther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen
Registergericht: Amtsgericht München HRB 6466
USt-IdNr: DE 129521671

___________________________________________________________
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