This is not tool specific. Instead, galaxy automatically unzips as files are uploaded. beware: it only supports one data set per zipped file - so gzipped fastqs are find.. but a tarball of a bunch of fastqs is not. Brad On Aug 21, 2012, at 10:23 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
Interesting...
Hans, could you specify what tools currently available in Galaxy support gzip'd fastq files?
Any in this list?: - Bowtie/Tophat - FastQC - FASTQ Groomer
Having the possibility to use these tools without needing to unzip fastq files would be great and I didn't know you could do that.
Thanks, Carlos
On Tue, Aug 21, 2012 at 3:16 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
moving to dev......
Hi Jen and Brandon
well, I don't agree (or maybe I misunderstood the question/answer):
we work a lot with compressed data (ie g'zipped fastq files from the sequencer), and link them as a Galaxy data library. We preselect 'fastq' as file format.
And then, the first tool in our NGS analysis expects a gzipped fastq file.
Regards, Hans
-------- Original Message -------- Subject: Re: [galaxy-user] Linking to Compressed Data Date: Mon, 20 Aug 2012 10:32:26 -0700 From: Jennifer Jackson <jen@bx.psu.edu> To: Branden Timm <btimm@wisc.edu> CC: <galaxy-user@lists.bx.psu.edu>
Hi Branden,
Data in a library needs to be uncompressed in order for Galaxy to index and have access to it correctly.
I updated our wiki for the "upload by filesystem link" option: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Good question!
Jen Galaxy team
On 8/15/12 9:09 AM, Branden Timm wrote:
Hi All, Is it possible to link to compressed files in a Galaxy data library? We receive all of our NGS data in bz2 or gzip format for obvious reasons, just wondering if I have to decompress it on the filesystem before I link to it or not. Thanks!
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