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Hi Hak,
The tool is called archive_datatypes written by cmonjeau and is
available in the Galaxy Main Tool shed.
And here is the trello card to vote for support of compressed
versions of standard data types.
https://trello.com/c/3RkTDnIn/345-666-support-gzipped-gz-compressed-versions-of-standard-datatypes
and was discussed here;
https://biostar.usegalaxy.org/p/13076/
Cheers,
Martin
On 09/06/2015 11:05 AM, Hakeem Almabrazi wrote:
>
> 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 <mailto: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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- --
- --
Dr. Martin Vickers
Data Manager/HPC Systems Administrator
Institute of Biological, Environmental and Rural Sciences
IBERS New Building
Aberystwyth University
w: http://www.martin-vickers.co.uk/
e: mjv08@aber.ac.uk
t: 01970 62 2807
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