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 <greg@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/... 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.molter@gmail.com <mailto:colin.molter@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 <eskirton@lbl.gov <mailto:eskirton@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 greg@bx.psu.edu
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