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.cock@googlemail.com wrote:
On Fri, Jan 20, 2012 at 12:42 PM, Leandro Hermida softdev@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/