On Sun, Nov 11, 2012 at 10:11 PM, Philipe Moncuquet
<philippe.m...@gmail.com> wrote:
> Hi dev,
> I have written a perl script to perform some complex demultiplexing of
> reads. It works well on my computer but the integration to Galaxy is a bit
> tricky since it's the first time for me.
> At one point my perl script generates a bunch of fasta files, I want all
> this fasta files to be compressed and I use a tar command within the script
> to do so. I am not sure how to do the same within the Galaxy execution.
> I think it might work out with the "from_work_dir" attributes of the output
> tag but I don't know exactly where my script should write these fasta files
> and compress them so that the archive could be retrieve.
> I don't know either what to put in the "format" attributes since gz is not
> in the supported datatype or is it ? Should I create a new datatype ? The
> ending point of my tool would be to have the user be able to download one
> compressed file that would contains all the sorted fasta files.
> Cheers,
> Philippe

There's an open issue "Support gzipped (*.gz) compressed versions of
standard datatypes" (which was issue 666 on bitbucket) for this topic:


Right now you'd have to manually define a new datatype, e.g.
gzipped-fasta, which is I believe how some groups are working
with gzipped-fastqsanger as a custom datatype for GZIP
compressed FASTQ files.


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