This is not tool specific.
Instead, galaxy automatically unzips as files are uploaded.

beware: it only supports one data set per zipped file - so gzipped fastqs are 
find.. but a tarball of a bunch of fastqs is not.


Brad
On Aug 21, 2012, at 10:23 AM, Carlos Borroto <carlos.borr...@gmail.com>
 wrote:

> Interesting...
> 
> Hans, could you specify what tools currently available in Galaxy
> support gzip'd fastq files?
> 
> Any in this list?:
> - Bowtie/Tophat
> - FastQC
> - FASTQ Groomer
> 
> Having the possibility to use these tools without needing to unzip
> fastq files would be great and I didn't know you could do that.
> 
> Thanks,
> Carlos
> 
> On Tue, Aug 21, 2012 at 3:16 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>> moving to dev......
>> 
>> 
>> Hi Jen and Brandon
>> 
>> well, I don't agree (or maybe I misunderstood the question/answer):
>> 
>> 
>> we work a lot with compressed data (ie g'zipped fastq files from the
>> sequencer), and link them as a Galaxy data library. We preselect 'fastq' as
>> file format.
>> 
>> And then, the first tool in our NGS analysis expects a gzipped fastq file.
>> 
>> 
>> Regards, Hans
>> 
>> 
>> 
>> -------- Original Message --------
>> Subject: Re: [galaxy-user] Linking to Compressed Data
>> Date: Mon, 20 Aug 2012 10:32:26 -0700
>> From: Jennifer Jackson <j...@bx.psu.edu>
>> To: Branden Timm <bt...@wisc.edu>
>> CC: <galaxy-u...@lists.bx.psu.edu>
>> 
>> Hi Branden,
>> 
>> Data in a library needs to be uncompressed in order for Galaxy to index
>> and have access to it correctly.
>> 
>> I updated our wiki for the "upload by filesystem link" option:
>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
>> 
>> Good question!
>> 
>> Jen
>> Galaxy team
>> 
>> On 8/15/12 9:09 AM, Branden Timm wrote:
>>> 
>>> Hi All,
>>>   Is it possible to link to compressed files in a Galaxy data library?
>>> We receive all of our NGS data in bz2 or gzip format for obvious
>>> reasons, just wondering if I have to decompress it on the filesystem
>>> before I link to it or not.  Thanks!
>>> 
>>> --
>>> Branden Timm
>>> bt...@glbrc.wisc.edu
>>> ___________________________________________________________
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>> 
>> 
>> --
>> Jennifer Jackson
>> http://galaxyproject.org
>> ___________________________________________________________
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> ___________________________________________________________
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--
Brad Langhorst
langho...@neb.com
978-380-7564





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