On May 16, 2012, at 9:47 AM, Peter Cock wrote:

> Hello all,
> 
> What is the current status in Galaxy for supporting compressed files?

Hi Peter,

Unfortunately, there's been nothing done on this so far.  I'd love to see it 
happen, but it hasn't been on the top of our priorities.

--nate

> We've talked about this before, for example in addition to FASTQ,
> many of us have expressed a wish to work with gzipped FASTQ.
> I understand that some have customized their local Galaxy
> installations to use gzipped FASTQ as a specific data type - I'm
> more interested in a general file format neutral solution.
> 
> Also, I'd like to be able to used BGZF (not just GZIP) because it
> is better for random access - see for example
> http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html
> - and makes it much easier to break up large datafiles for sharing
> over a cluster (i.e. it could be exploited in the current Galaxy code
> for splitting large sequence files).
> 
> The 11 May 2012 Galaxy Development News Brief
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-May/009757.html
> mentions tabix indexing - that uses bgzip, so is there something
> general in place yet to allow tool wrappers to say they accept not just
> given file formats, but different compressed versions of file formats?
> 
> Ideally I'd like to be able to write an XML tool description saying
> a tool produced BGZF compressed tabular data, or GZIP
> compressed Sanger FASTQ etc. Similarly, I'd like to specify my
> tool accepts FASTA or gzipped FASTA (including BGZF FASTA).
> While for older tools if they say they accept only uncompressed
> FASTA, Galaxy could automatically decompress any compressed
> FASTA entries in my history on demand.
> 
> Peter
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