Moving Histories from old to new Galaxy build
Hi all. We are moving from an old version of Galaxy (build: 1349) to the current one; we know there is a big gap in between Im wondering if there is a way to move in just one unpainful step all the saved histories from the old version to the new one, or alternatively to download/save entire histories at once from the old and then reload them to the new build. Any other ideas? Thank you a lot for your help! Lucilla
Lucilla why don't you just upgrade your old Galaxy installation? Doing an upgrade (even a big step) is pretty much painless. Of course it depends on how much customization you have introduced. If in doubt, clone your installation (ie file system and database), and try the upgrade first with the clone. Regards, Hans On 09/01/2010 12:07 PM, Lucilla Luzi wrote:
Hi all. We are moving from an old version of Galaxy (build: 1349) to the current one; we know there is a big gap in between… I’m wondering if there is a way to move in just one unpainful step all the saved histories from the old version to the new one, or alternatively to download/save entire histories at once from the old and then reload them to the new build.
Any other ideas?
Thank you a lot for your help! Lucilla
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hans, thank you a lot for your prompt answer. Actually, the story it is a bit more complicated then I previously summarized and my description was somewhere incomplete but I don't want to bother you too much with my (brainless) troubles. We indeed cloned and upgraded our installation (let's call it version2), exactly as you suggested, mainly to test if a custom package we developed in Galaxy was still properly working in the new build. We in fact succeed in this task and also to correctly move the old histories to the new Galaxy version. Therefore, still maintaining operative the old one (let's call it version1), we asked some users to use the new build to test it. Finally, since we checked that everything is right, we would like to definitively move to the new build (repeating cloning and upgrading of the version1 that was, meanwhile still working) generating the definitive version3. But at this point we would also like to recover and move the histories of the "tester users", who worked on the version2, to the version3. Indeed the questions of my previous mail now become more general: do exist a way to export a history or multiple files of a history at once from the system? I'm thinking to a procedure that the final user could use from him-/her-self through the web interface. Also in my personal experience, I noticed that it is so easy and fast to produce files in Galaxy that very soon the working history becomes full up of files and it is very boring to save singularly each of them. Don't you think it would be very useful to have the chance to download and save, as multiple files, the entire history in one click? And useful, as well, couldn't be upload multiple files at once? These two actions would rapidly resolve our problem, too. Thank a lot [and sorry for my disordered and tortuous thinks]. Lucilla At 13:50 01 09 2010, Hans-Rudolf Hotz wrote:
Lucilla
why don't you just upgrade your old Galaxy installation?
Doing an upgrade (even a big step) is pretty much painless. Of course it depends on how much customization you have introduced.
If in doubt, clone your installation (ie file system and database), and try the upgrade first with the clone.
Regards, Hans
On 09/01/2010 12:07 PM, Lucilla Luzi wrote:
Hi all. We are moving from an old version of Galaxy (build: 1349) to the current one; we know there is a big gap in between Im wondering if there is a way to move in just one unpainful step all the saved histories from the old version to the new one, or alternatively to download/save entire histories at once from the old and then reload them to the new build.
Any other ideas?
Thank you a lot for your help! Lucilla
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Lucilla ok, now I understand your problem. Have you tried the History option "Export to File", followed by "Import from File" ? This allows you to download/upload all files (and meta data) of one history. So in your case: your 'tester users' have to exoprt each of his/her history in "version2" separately followed by "Import from File" in "version3" ? Hope this helps, Hans On 09/01/2010 05:57 PM, Lucilla Luzi wrote:
Hans,
thank you a lot for your prompt answer.
Actually, the story it is a bit more complicated then I previously summarized and my description was somewhere incomplete but I don't want to bother you too much with my (brainless) troubles.
We indeed cloned and upgraded our installation (let's call it version2), exactly as you suggested, mainly to test if a custom package we developed in Galaxy was still properly working in the new build.
We in fact succeed in this task and also to correctly move the old histories to the new Galaxy version. Therefore, still maintaining operative the old one (let's call it version1), we asked some users to use the new build to test it.
Finally, since we checked that everything is right, we would like to definitively move to the new build (repeating cloning and upgrading of the version1 that was, meanwhile still working) generating the definitive version3. But at this point we would also like to recover and move the histories of the "tester users", who worked on the version2, to the version3.
Indeed the questions of my previous mail now become more general: do exist a way to export a history or multiple files of a history at once from the system? I'm thinking to a procedure that the final user could use from him-/her-self through the web interface.
Also in my personal experience, I noticed that it is so easy and fast to produce files in Galaxy that very soon the working history becomes full up of files and it is very boring to save singularly each of them.
Don't you think it would be very useful to have the chance to download and save, as multiple files, the entire history in one click? And useful, as well, couldn't be upload multiple files at once? These two actions would rapidly resolve our problem, too.
Thank a lot [and sorry for my disordered and tortuous thinks]. Lucilla
At 13:50 01 09 2010, Hans-Rudolf Hotz wrote:
Lucilla
why don't you just upgrade your old Galaxy installation?
Doing an upgrade (even a big step) is pretty much painless. Of course it depends on how much customization you have introduced.
If in doubt, clone your installation (ie file system and database), and try the upgrade first with the clone.
Regards, Hans
On 09/01/2010 12:07 PM, Lucilla Luzi wrote:
Hi all. We are moving from an old version of Galaxy (build: 1349) to the current one; we know there is a big gap in between… I’m wondering if there is a way to move in just one unpainful step all the saved histories from the old version to the new one, or alternatively to download/save entire histories at once from the old and then reload them to the new build.
Any other ideas?
Thank you a lot for your help! Lucilla
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Hans and Lucilla, Sorry for the slow reply.
Have you tried the History option "Export to File", followed by "Import from File" ? This allows you to download/upload all files (and meta data) of one history.
Unfortunately, this functionality isn't yet finished and is disabled by default. We're hoping to have this functionality working in the next 6 weeks or so. In the meantime, you can enable it, but it's not very robust right now and will likely only work with small histories. Let me know if you'd like instructions to enable it. Best, J.
Hans and Jeremy, thank you both very much for your answers! We'll try to enable the Export functionality, as you suggest, even if not yet finished, and we'll see if we can manage to resolve our problems, looking forward to the completion of these very useful functions ;). (thank you to the all Galaxy team: your're doing a fantastic job!) Best regards Lu At 01:55 03 09 2010, Jeremy Goecks wrote:
Hi Hans and Lucilla,
Sorry for the slow reply.
Have you tried the History option "Export to File", followed by "Import from File" ? This allows you to download/upload all files (and meta data) of one history.
Unfortunately, this functionality isn't yet finished and is disabled by default. We're hoping to have this functionality working in the next 6 weeks or so.
In the meantime, you can enable it, but it's not very robust right now and will likely only work with small histories. Let me know if you'd like instructions to enable it.
Best, J.
participants (3)
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Hans-Rudolf Hotz -
Jeremy Goecks -
Lucilla Luzi