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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