Hi Peter,

Sorry I wasn't clear, the .gz gets stripped from the name in the
Galaxy UI when you upload the files into a data library via the manage
data libraries form. When you upload it via Get Data -> Upload File
the .gz is preserved which is what one would want since I am not
having it gunzipped by specifying its own new datatype and extension
and changing binary.py to make sure it doesn't fall through to the
elsif where it tries to unzip stuff.

On Fri, Jan 20, 2012 at 2:25 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Fri, Jan 20, 2012 at 12:42 PM, Leandro Hermida
> <soft...@leandrohermida.com> wrote:
>> Hello,
>> We've created a new binary datatype for .fastq.gz files following the
>> same methodology as the BAM files since we don't want our fasta.gz
>> files to be gunzipped.  I added the appropriate code in upload.py to
>> make sure of this.  This new datatype and extension successfully does
>> not gunzip our files.  But when we upload it into a data library via
>> the data library "Upload via filesystem paths" it for some reason
>> automatically strips the .gz part out. When we take the same .fastq.gz
>> file and upload it via Get Data -> Upload File it works fine, nothing
>> is stripped from file name. Where is it doing this and how can prevent
>> from stripping the .gz via the data library menus?
> I thought Galaxy would usually try to replace the extension
> with *.dat for any file type when uploaded?
> Peter
> P.S. Is anyone working on the more general solution of
> supporting a gzipped version of (almost) any Galaxy datatype?
> https://bitbucket.org/galaxy/galaxy-central/issue/666/

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to