Hi Greg,
Has Steve's gls script made it into ~/contrib of the Galaxy distribution?
I'd love to try it out as I'm having issues with the helper.py script giving
me false IDs.
Thanks,
Matt
On Fri, Sep 2, 2011 at 9:18 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello Steve,
>
> Thanks for making this available. If you could email me the script, I'll
> include it in the ~/contrib directory in the Galaxy distribution.
>
> Greg Von Kuster
>
> On Sep 2, 2011, at 3:20 AM, Steve Taylor wrote:
>
> > Hi,
> >
> > We have written a tool that we call gls ("galaxy ls"). Running it is
> similar to doing "ls -ltr" in that it lists the histories in reverse
> chronological order and shows the actual path of the .dat file on the file
> system. You can then symlink/copy the actual files.
> >
> > Example output:
> >
> > 2011-03-08 14:29:18 - Test 1
> > 2011-03-08 14:29:56 - CXXC.bed
> /galaxy/database/files/001/dataset_1749.dat
> > 2011-03-16 14:08:00 - BED-to-GFF on data 1
> /galaxy/database/files/001/dataset_1750.dat
> >
> > 2011-06-17 12:13:28 - Test 2
> > 2011-06-17 12:14:24 - UCSC Main on Chicken: refGene (genome)
> /galaxy/database/files/003/dataset_3085.dat
> > 2011-06-17 12:51:02 - UCSC Main on Chicken: refGene
> (chr2:57311158-57314247) /galaxy/database/files/003/dataset_3086.dat
> >
> > 2011-07-27 07:12:30 - Test 3
> > 2011-07-27 07:15:44 -
> http://www.molbiol.ox.ac.uk/data/biopivot/example/small/example.gff3/galaxy/database/files/003/dataset_3296.dat
> > 2011-07-27 07:16:27 - annotated gff3 on data 1
> /galaxy/database/files/003/dataset_3297.dat
> > 2011-07-27 07:18:42 - UCSC Main on Human: eponine (genome)
> /galaxy/database/files/003/dataset_3298.dat
> > 2011-07-27 07:19:38 - annotated overlap gff3 on data 3 and data 2
> /galaxy/database/files/003/dataset_3299.dat
> > 2011-08-10 07:35:20 - SLX-3645.591.s_4_Input_AB_peaks.txt
> /galaxy/database/files/004/dataset_4086.dat
> > 2011-08-10 07:55:48 - macs2gff3 on data 5
> /galaxy/database/files/004/dataset_4088.dat
> > 2011-08-10 07:56:37 - annotated gff3 on data 7
> /galaxy/database/files/004/dataset_4089.dat
> >
> >
> > It's written in Perl, is run from the command line and accesses the
> galaxy database. We are happy to make this available if there is interest.
> Is the Tool Shed the best place to put it given it isn't a wrapper?
> >
> > Regards,
> >
> > Steve
> >
> >
> >> On Thu, Aug 4, 2011 at 9:57 PM, colin molter <colin.mol...@gmail.com
> >> <mailto:colin.mol...@gmail.com>> wrote:
> >> > Is there a way to directly move/copy data from your galaxy history to
> a
> >> > given location in the filesystem of the same galaxy server?
> >>
> >> 2011/9/1 Edward Kirton <eskir...@lbl.gov <mailto:eskir...@lbl.gov>>
> >>
> >> why not create a simple "export" tool? perhaps with the option to cp
> >> or symlink.
> >>
> >>
> >> This is exactly what I would like to have. I checked on Shed Tool. But
> >> it seems that that tool doesn't exist yet. Before to try to make that
> >> tool, I wanted to be sure that nobody had a similar tool for sharing.
> >> thx
> >> colin
> > ___________________________________________________________
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>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>
> ___________________________________________________________
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>
--
Matthew Conte
Bioinformatician
Department of Biology
University of Maryland
mco...@umd.edu
Bouillabase.org
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