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 <j...@bx.psu.edu>
To: Branden Timm <bt...@wisc.edu>
CC: <galaxy-u...@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!
--
Branden Timm
bt...@glbrc.wisc.edu
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--
Jennifer Jackson
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