Thank you Martin for your reply.

 

I will give it a try.  Can you please send me the name of the tool you are referring to?

 

Also, I am hoping others will be able to share their insights about the other concerns in my post.

 

Regards,

 

From: Martin Vickers [mjv08] [mailto:mjv08@aber.ac.uk]
Sent: Saturday, September 05, 2015 12:31 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] loading with Auto detect and fastqsanger options issue!

 

Hi Hak,

 

I noticed the same thing when linking them when adding fastq.gz files as a data library. The auto detect was reading the whole file as it was unknown, presumably looking for some sort of characteristic to place it. What I did to resolve this was add the archive data format data type from the tool shed which included fastq.gz. This meant that auto detect instantly found the correct type. Finally I added the gunzip tool to galaxy and it works well. 

 

There is also a trello feature request asking for this to be inbuilt of if you're interested you may wish to vote for it. I will forward you the like when I'm back at a computer. 

 

Hope that helps,

 

Martin 

Sent on the move.


On 4 Sep 2015, at 19:04, Hakeem Almabrazi <halmabrazi@sidra.org> wrote:

Hi,

 

I have installed Galaxy as cluster in my local env.  I have few fastq.gz files in my file system that I want to link them to galaxy instead of loading them.  When I select “Auto Detect” during the loading I noticed two things.

 

First, it is taking way longer to link the files with the AutoDetect option compared to when I chose Fastqsanger as my file type.  It takes less than a second if I specify the type, i.e Fastqsanger.   Any reason why is that?  Is there a way to speed up the first option (Auto Detect)?

 

Second, when it finish linking for AutoDetect option, it shows the DataType for these files as “data” rather than fastq files. 

Does this mean my fastq.gz files are not recognize as fastq files?

 

To validate my fastq files, I tried to use FastqValidator tool I get an error saying “BGZF EOF marker is missing”.  How can I fix these files?

 

I appreciate any kind of help,

 

Regards,

Hak

 

 

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