pt
>
> 2. Put the BAM in the only order galaxy will accept.
>
> Christian
> University of Manchester
> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
> Amelia Ireland [airel...@lbl.gov]
> Sent: Wednesday, March 23, 2016 8:24 PM
> To: Daniel Blank
t;
> Christian
> University of Manchester
> --
> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf
> of Amelia Ireland [airel...@lbl.gov]
> *Sent:* Wednesday, March 23, 2016 8:24 PM
> *To:* Daniel Blankenberg
> *Cc:* galaxy-dev@lists.galaxyproject.org
>
: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Amelia Ireland [airel...@lbl.gov]
Sent: Wednesday, March 23, 2016 8:24 PM
To: Daniel Blankenberg
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Troubleshooting BAM file upload issues
I'm using the sta
I'm using the standard 'Upload file' tool, and choosing some local files. I
can successfully upload these files to the galaxy installation on my laptop
and to the usegalaxy.org server, but uploading them to the galaxy
installation on the server results in their appearing to be empty and the
error m
Hi Amelia,
How are you uploading the files?
If you are using a copy and pasted URL, can you make sure that the example file
exists and is accessible to the machine where the Galaxy job is running.
A 404 error, for example, can often masquerade as a “The uploaded file contains
inappropriate H
On 23 March 2016 at 01:00, Björn Grüning wrote:
> Hi Amelia,
>
> can you pleae check if you have samtools installed in your PATH?
>
I've got it in my tool dependencies dir and it's also available as an
Environment module.
The tools dependencies file looks like this:
Debug me
Both, unfortunately.
On 23 Mar 2016 00:41, "Hans-Rudolf Hotz" wrote:
> Hi Amelia
>
> Does this happen with "Auto-detect" or do you pre-set the data type to
> 'bam' ?
>
>
> Regards, Hans-Rudolf
>
>
> On 03/22/2016 07:28 PM, Amelia Ireland wrote:
>
>> I'm setting up a Galaxy instance on a new serve
: Amelia Ireland; galaxy-dev@u coordinateslists.galaxyproject.org
Subject: Re: [galaxy-dev] Troubleshooting BAM file upload issues
Hi Amelia,
can you pleae check if you have samtools installed in your PATH?
Ciao,
Bjoern
Am 22.03.2016 um 19:28 schrieb Amelia Ireland:
> I'm setting up a Galaxy
Hi Amelia,
can you pleae check if you have samtools installed in your PATH?
Ciao,
Bjoern
Am 22.03.2016 um 19:28 schrieb Amelia Ireland:
> I'm setting up a Galaxy instance on a new server and am having some
> issues with BAM file uploads. I'm using the BAM files supplied with
> JBrowse for testin
Hi Amelia
Does this happen with "Auto-detect" or do you pre-set the data type to
'bam' ?
Regards, Hans-Rudolf
On 03/22/2016 07:28 PM, Amelia Ireland wrote:
I'm setting up a Galaxy instance on a new server and am having some
issues with BAM file uploads. I'm using the BAM files supplied wit
I'm setting up a Galaxy instance on a new server and am having some issues
with BAM file uploads. I'm using the BAM files supplied with JBrowse for
testing purposes. I have Galaxy installed on my laptop and file uploads are
working fine, so it's evidently an issue with the server and/or OS
configur
Hello Peter,
Thanks a lot. It worked well. However the run stopped after a few minutes.
Here is the message :
Error aligning sequence. Error reading ebwt array: returned 113175904,
length was 823263360 Your index files may be corrupt; please try
re-building or re-downloading. A complete index consi
Hi Lionel
Sounds like Galaxy does not know what format your FASTQ file is. When you
click on it, what format does it show? Is it simple fastq? And how did you
get it into Galaxy?
You might need to manually specify the format by clicking on the Edit
Attributes button (the pencil icon) and select t
Hello,
I have a problem when I try to align en FATSQ file for a ChIP-seq.
I have done a FASTQ grooming because it has been performed on Illumina. No
my file is a .FASTSANGER.
However my file is not recognized. I see this : No fastqsanger,
fastqillumina or fastqsolexa dataset collection available.
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