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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