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)
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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
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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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