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 
<halmabr...@sidra.org<mailto:halmabr...@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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