On Sun, Nov 11, 2012 at 10:11 PM, Philipe Moncuquet <philippe.mcqt@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: https://trello.com/card/666-support-gzipped-gz-compressed-versions-of-standa... 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. Regards, Peter