HOW TO RETRIEVE DATA FROM HISTORY??!!
Hi all, i am still stuck with the same problem. 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? Said differently, there is a nice way to import data from the server to galaxy, is it possible to do the reverse? So far, I am obliged to download the file from galaxy to my client machine and then back to the server!!!! with huge bam files of 3Gb it is not so convenient!! thank you all colin
why not create a simple "export" tool? perhaps with the option to cp or symlink. On Thu, Aug 4, 2011 at 9:57 PM, colin molter <colin.molter@gmail.com> wrote:
Hi all, i am still stuck with the same problem. 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? Said differently, there is a nice way to import data from the server to galaxy, is it possible to do the reverse? So far, I am obliged to download the file from galaxy to my client machine and then back to the server!!!! with huge bam files of 3Gb it is not so convenient!! thank you all colin
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On Thu, Aug 4, 2011 at 9:57 PM, colin molter <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>
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
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
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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
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:
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:
-- Matthew Conte Bioinformatician Department of Biology University of Maryland mconte@umd.edu Bouillabase.org
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:
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:
-- 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
participants (5)
-
colin molter -
Edward Kirton -
Greg Von Kuster -
Matthew Conte -
Steve Taylor