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 [johns198@umn.edu] Sent: Friday, November 29, 2013 10:35 PM To: Vosberg, Sebastian; jrobinso@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-request@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.vosberg@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: 20854588711E4A489A3AD70C9BA5548A01AE291C4614@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 jrobinso@broadinstitute.org To: "Vosberg, Sebastian" sebastian.vosberg@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: 5298A7E2.7000908@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
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