Re: [galaxy-dev] [galaxy-bugs] tool updates for local installation
Helo Ravi, please send all questions to one of the Galaxy mail lists as sending to personal emails will usually not generate responses. I've forwarded your question to the dev list since I am not involved in the Galaxy cloud development efforts. On Jun 17, 2011, at 5:47 PM, Sanka, Ravi wrote:
Hello Greg,
Thank you for your quick response. I have another, related question.
I understand that there is an Amazon-Cloud version of Galaxy called CloudMan, where tool updates are taken care of for the users.
Does CloudMan take care of its own updates? If so, how often do the tools get updated?
----------------------------------------------- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -----------------------------------------------
From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: Friday, June 17, 2011 3:24 PM To: Sanka, Ravi Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] tool updates for local installation
Hello Ravi,
At the current time, it is up to the owner of the Galaxy instance to look at the Galaxy tool shed for updates, and pull them to their local instance. Regarding 3rd party dependencies, it is again the responsibility of the owner of the Galaxy instance to handle the dependencies. This will change at some point in the future, at which point we'll let you know of the changes.
Thanks for your interest!
Greg Von Kuster
On Jun 17, 2011, at 3:02 PM, Sanka, Ravi wrote:
Greetings,
My name is Ravi Sanka. I have a question for maintaining tools on a local installation of Galaxy.
What happens one or more updates are available for the tools that are part of the Galaxy community? Is it the client’s responsibility to search for updates of each tool on his install? Or do update alerts get sent by Galaxy to keep the tools at the most recent version?
And what about those tools that are part of the Galaxy community but use third-party software (i.e. NCBI Blast+)? Is it the same for them, or does a different procedure apply?
Thanks, - Ravi Sanka
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Ravi, CloudMan does handle the updates but it is not necessarily automatic. Namely, once you create a Galaxy CloudMan instance, the settings and tool versions used at that version will remain the same. If/when we release an official update for Galaxy and/or tools, it is possible to point your instance to use the updated versions by manually editing instance's configuration files. We handle the updates this way because it ensures complete reproducibility of results. As far as the frequency of updates - we don't have a strict schedule but, on average, Galaxy gets updated about once a month and tools get updated after there has been enough new tool versions released to warrant an update. This can be changed though. Also, you can perform your own updates to the tools and it is possible to persist those changes. Enis On Sun, Jun 19, 2011 at 11:18 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Helo Ravi, please send all questions to one of the Galaxy mail lists as sending to personal emails will usually not generate responses. I've forwarded your question to the dev list since I am not involved in the Galaxy cloud development efforts.
On Jun 17, 2011, at 5:47 PM, Sanka, Ravi wrote:
Hello Greg,**** ** ** Thank you for your quick response. I have another, related question.**** ** ** I understand that there is an Amazon-Cloud version of Galaxy called CloudMan, where tool updates are taken care of for the users.**** ** ** Does CloudMan take care of its own updates? If so, how often do the tools get updated?**** ** ** -----------------------------------------------**** Ravi Sanka**** ICS - Bioinformatics Engineer**** J. Craig Venter Institute**** 301-795-7743**** -----------------------------------------------**** ** ** *From:* Greg Von Kuster [mailto:greg@bx.psu.edu] *Sent:* Friday, June 17, 2011 3:24 PM *To:* Sanka, Ravi *Cc:* galaxy-bugs@bx.psu.edu *Subject:* Re: [galaxy-bugs] tool updates for local installation**** ** ** Hello Ravi,**** ** ** At the current time, it is up to the owner of the Galaxy instance to look at the Galaxy tool shed for updates, and pull them to their local instance. Regarding 3rd party dependencies, it is again the responsibility of the owner of the Galaxy instance to handle the dependencies. This will change at some point in the future, at which point we'll let you know of the changes.**** ** ** Thanks for your interest!**** ** ** Greg Von Kuster**** ** ** On Jun 17, 2011, at 3:02 PM, Sanka, Ravi wrote:****
**** Greetings,**** **** My name is Ravi Sanka. I have a question for maintaining tools on a local installation of Galaxy.**** **** What happens one or more updates are available for the tools that are part of the Galaxy community? Is it the client’s responsibility to search for updates of each tool on his install? Or do update alerts get sent by Galaxy to keep the tools at the most recent version?**** **** And what about those tools that are part of the Galaxy community but use third-party software (i.e. NCBI Blast+)? Is it the same for them, or does a different procedure apply?**** **** Thanks,**** - Ravi Sanka**** **** ** ** ** ** ** ** Greg Von Kuster**** Galaxy Development Team**** greg@bx.psu.edu**** ** ** ** ** ** **
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
participants (2)
-
Enis Afgan -
Greg Von Kuster