Not what I was hoping for. I usually link without copying into galaxy, so it won't help me. I also got excited because I thought there was the possibility of working with fastq files without having to keep unzipped datasets, that would safe a lot of space, even if processing gets slower.
Hans, I might take a look at modifying Galaxy underlying code, but in general I'm not fun of keeping up with my own custom code. Thanks, Carlos On Tue, Aug 21, 2012 at 11:04 AM, Langhorst, Brad <[email protected]> wrote: > 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 <[email protected]> > 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 <[email protected]> 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 <[email protected]> >>> To: Branden Timm <[email protected]> >>> CC: <[email protected]> >>> >>> 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 >>>> [email protected] >>>> ___________________________________________________________ >>>> The Galaxy User list should be used for the discussion of >>>> Galaxy analysis and other features on the public server >>>> at usegalaxy.org. Please keep all replies on the list by >>>> using "reply all" in your mail client. For discussion of >>>> local Galaxy instances and the Galaxy source code, please >>>> use the Galaxy Development list: >>>> >>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>>> >>>> To manage your subscriptions to this and other Galaxy lists, >>>> please use the interface at: >>>> >>>> http://lists.bx.psu.edu/ >>> >>> >>> -- >>> Jennifer Jackson >>> http://galaxyproject.org >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >>> >>> ___________________________________________________________ >>> >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > -- > Brad Langhorst > [email protected] > 978-380-7564 > > > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
