Hello Matt,

Steve's script has not yet made it to the distribution, although it should be available there within the next few weeks.  If you need it sooner, you'll have to pull it from galaxy central.  Sorry for the inconvenience.

Greg Von Kuster

On Sep 27, 2011, at 4:18 PM, Matthew Conte wrote:

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/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.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
> ___________________________________________________________
> 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/

Greg Von Kuster
Galaxy Development Team
greg@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/



--
Matthew Conte
Bioinformatician
Department of Biology
University of Maryland
mconte@umd.edu
Bouillabase.org

___________________________________________________________
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/

Greg Von Kuster
Galaxy Development Team
greg@bx.psu.edu