Re: [galaxy-dev] Configuration of a local install - mi-deploy ?
Hi Greg & Ross, Thanks for this! Yes, I confused the issue by mentioning the Tool Shed, sorry - it's the binaries themselves I need to install. Essentially I think I need to follow the steps at http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup , but I was wondering about mi-deployment scripts as a better way to do this, and whether that's standard practice. After looking through the scripts they really seem like the best option to me - it looks like they are set up so you mostly only need to change configuration variables to get this to work. The scripts are mentioned on the wiki instructions but don't seem to be the default option (they are not bundled in galaxy-dist), so I wondered if people are usually doing it this way? Thanks, Clare On Fri, Nov 11, 2011 at 2:06 AM, Ross <ross.lazarus@gmail.com> wrote:
Clare,
As Greg says, the tool wrappers exposed on Main all come with a mercurial checkout - but all the binary dependencies, genomic data and indexes do not. The tool shed is really the tool-wrapper shed - binary and data dependencies aren't there either.
I haven't tried them but I'd guess that the deploy scripts take care of a lot of messy details but will probably need some work to fit your local setup.
As to email for admin - my advice would be don't worry about it - if one user forgets their password you can reset it from the admin interface - that's the main use and if this is really a test instance, it's not a show stopper.
On Thu, Nov 10, 2011 at 9:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Clare,
On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote:
Hi all,
Most of our playing around with Galaxy has been in getting it working on our local cloud, but now for the first time I'm configuring a non-cloud local install of galaxy-dist (set up as per http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server)
So I have some naive questions!
Would it be a sensible approach to grab the tools_fabfile script from mi-deployment and use it in this case? Or should I be using the Tool Shed for installing the base set of tools?
The Galaxy distribution includes all of the tools you see on both the Penn State test and main instances. You can also get tools form the tool shed if you want - see our wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed for information about how to do this. I don't think you'll need to use the tools_fabfile script from mi_deployment repo for your local instance.
Also, if I have problems with this server sending out emails (which may be the case) am I going to run into trouble with user/password management or can I just admin everything manually? There will only be a very small number of users on this server.
I'm not clear on this question, but you certainly shouldn't run into any problems with user / password management within Galaxy. From the Galaxy Admin interface you have the ability to "Manage users" where you can reset passwords if necessary.
If I have missed any good 'getting started' documentation on config/admin of a local install please point me in the right direction. I've been looking at http://wiki.g2.bx.psu.edu/Admin .
You found the right wiki.
Thanks, Clare
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759
Hi Clare, I misunderstood your initial questions, but with your details below, it's clear you would benefit from using tools_fabfile from mi_deployment, which sets up all the binary dependencies not included with Galaxy. As you mention, you may need to tweak the config settings. On Nov 10, 2011, at 8:09 PM, Clare Sloggett wrote:
Hi Greg & Ross,
Thanks for this!
Yes, I confused the issue by mentioning the Tool Shed, sorry - it's the binaries themselves I need to install. Essentially I think I need to follow the steps at http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup , but I was wondering about mi-deployment scripts as a better way to do this, and whether that's standard practice.
After looking through the scripts they really seem like the best option to me - it looks like they are set up so you mostly only need to change configuration variables to get this to work.
The scripts are mentioned on the wiki instructions but don't seem to be the default option (they are not bundled in galaxy-dist), so I wondered if people are usually doing it this way?
Thanks, Clare
On Fri, Nov 11, 2011 at 2:06 AM, Ross <ross.lazarus@gmail.com> wrote:
Clare,
As Greg says, the tool wrappers exposed on Main all come with a mercurial checkout - but all the binary dependencies, genomic data and indexes do not. The tool shed is really the tool-wrapper shed - binary and data dependencies aren't there either.
I haven't tried them but I'd guess that the deploy scripts take care of a lot of messy details but will probably need some work to fit your local setup.
As to email for admin - my advice would be don't worry about it - if one user forgets their password you can reset it from the admin interface - that's the main use and if this is really a test instance, it's not a show stopper.
On Thu, Nov 10, 2011 at 9:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Clare,
On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote:
Hi all,
Most of our playing around with Galaxy has been in getting it working on our local cloud, but now for the first time I'm configuring a non-cloud local install of galaxy-dist (set up as per http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server)
So I have some naive questions!
Would it be a sensible approach to grab the tools_fabfile script from mi-deployment and use it in this case? Or should I be using the Tool Shed for installing the base set of tools?
The Galaxy distribution includes all of the tools you see on both the Penn State test and main instances. You can also get tools form the tool shed if you want - see our wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed for information about how to do this. I don't think you'll need to use the tools_fabfile script from mi_deployment repo for your local instance.
Also, if I have problems with this server sending out emails (which may be the case) am I going to run into trouble with user/password management or can I just admin everything manually? There will only be a very small number of users on this server.
I'm not clear on this question, but you certainly shouldn't run into any problems with user / password management within Galaxy. From the Galaxy Admin interface you have the ability to "Manage users" where you can reset passwords if necessary.
If I have missed any good 'getting started' documentation on config/admin of a local install please point me in the right direction. I've been looking at http://wiki.g2.bx.psu.edu/Admin .
You found the right wiki.
Thanks, Clare
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759
___________________________________________________________ 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 Clare, As a technical add-on - you didn't mention what type OS you're looking to install this on so I just wanted to mention that mi-deployment scripts are tested primarily on Ubuntu 10.04 LTS and thus most likely to work properly there. If you're also looking to setup the data, unfortunately the data script is fairly well out of date at this point so I am not sure how it will work. Instead, you can try using this script https://github.com/chapmanb/cloudbiolinux/blob/master/data_fabfile.py. Enis On Fri, Nov 11, 2011 at 2:09 AM, Clare Sloggett <sloc@unimelb.edu.au> wrote:
Hi Greg & Ross,
Thanks for this!
Yes, I confused the issue by mentioning the Tool Shed, sorry - it's the binaries themselves I need to install. Essentially I think I need to follow the steps at http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup , but I was wondering about mi-deployment scripts as a better way to do this, and whether that's standard practice.
After looking through the scripts they really seem like the best option to me - it looks like they are set up so you mostly only need to change configuration variables to get this to work.
The scripts are mentioned on the wiki instructions but don't seem to be the default option (they are not bundled in galaxy-dist), so I wondered if people are usually doing it this way?
Thanks, Clare
On Fri, Nov 11, 2011 at 2:06 AM, Ross <ross.lazarus@gmail.com> wrote:
Clare,
As Greg says, the tool wrappers exposed on Main all come with a mercurial checkout - but all the binary dependencies, genomic data and indexes do not. The tool shed is really the tool-wrapper shed - binary and data dependencies aren't there either.
I haven't tried them but I'd guess that the deploy scripts take care of a lot of messy details but will probably need some work to fit your local setup.
As to email for admin - my advice would be don't worry about it - if one user forgets their password you can reset it from the admin interface - that's the main use and if this is really a test instance, it's not a show stopper.
On Thu, Nov 10, 2011 at 9:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Clare,
On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote:
Hi all,
Most of our playing around with Galaxy has been in getting it working on our local cloud, but now for the first time I'm configuring a non-cloud local install of galaxy-dist (set up as per http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server )
So I have some naive questions!
Would it be a sensible approach to grab the tools_fabfile script from mi-deployment and use it in this case? Or should I be using the Tool Shed for installing the base set of tools?
The Galaxy distribution includes all of the tools you see on both the Penn State test and main instances. You can also get tools form the tool shed if you want - see our wiki at http://wiki.g2.bx.psu.edu/Tool%20Shedfor information about how to do this. I don't think you'll need to use the tools_fabfile script from mi_deployment repo for your local instance.
Also, if I have problems with this server sending out emails (which may be the case) am I going to run into trouble with user/password management or can I just admin everything manually? There will only be a very small number of users on this server.
I'm not clear on this question, but you certainly shouldn't run into any problems with user / password management within Galaxy. From the Galaxy Admin interface you have the ability to "Manage users" where you can reset passwords if necessary.
If I have missed any good 'getting started' documentation on config/admin of a local install please point me in the right direction. I've been looking at http://wiki.g2.bx.psu.edu/Admin .
You found the right wiki.
Thanks, Clare
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759
___________________________________________________________ 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:
Hi Enis, Thanks, that's great - I actually didn't know about the cloudbiolinux version. It has the yaml configuration functionality which is nice. It looks to me like the one I was looking at in the virtualbox image was actually based on this one, which makes sense if the Amazon image contains both cloudbiolinux and cloudman. Thanks, Clare On Fri, Nov 11, 2011 at 7:35 PM, Enis Afgan <afgane@gmail.com> wrote:
Hi Clare, As a technical add-on - you didn't mention what type OS you're looking to install this on so I just wanted to mention that mi-deployment scripts are tested primarily on Ubuntu 10.04 LTS and thus most likely to work properly there. If you're also looking to setup the data, unfortunately the data script is fairly well out of date at this point so I am not sure how it will work. Instead, you can try using this script https://github.com/chapmanb/cloudbiolinux/blob/master/data_fabfile.py. Enis
On Fri, Nov 11, 2011 at 2:09 AM, Clare Sloggett <sloc@unimelb.edu.au> wrote:
Hi Greg & Ross,
Thanks for this!
Yes, I confused the issue by mentioning the Tool Shed, sorry - it's the binaries themselves I need to install. Essentially I think I need to follow the steps at http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup , but I was wondering about mi-deployment scripts as a better way to do this, and whether that's standard practice.
After looking through the scripts they really seem like the best option to me - it looks like they are set up so you mostly only need to change configuration variables to get this to work.
The scripts are mentioned on the wiki instructions but don't seem to be the default option (they are not bundled in galaxy-dist), so I wondered if people are usually doing it this way?
Thanks, Clare
On Fri, Nov 11, 2011 at 2:06 AM, Ross <ross.lazarus@gmail.com> wrote:
Clare,
As Greg says, the tool wrappers exposed on Main all come with a mercurial checkout - but all the binary dependencies, genomic data and indexes do not. The tool shed is really the tool-wrapper shed - binary and data dependencies aren't there either.
I haven't tried them but I'd guess that the deploy scripts take care of a lot of messy details but will probably need some work to fit your local setup.
As to email for admin - my advice would be don't worry about it - if one user forgets their password you can reset it from the admin interface - that's the main use and if this is really a test instance, it's not a show stopper.
On Thu, Nov 10, 2011 at 9:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Clare,
On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote:
Hi all,
Most of our playing around with Galaxy has been in getting it working on our local cloud, but now for the first time I'm configuring a non-cloud local install of galaxy-dist (set up as per
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server)
So I have some naive questions!
Would it be a sensible approach to grab the tools_fabfile script from mi-deployment and use it in this case? Or should I be using the Tool Shed for installing the base set of tools?
The Galaxy distribution includes all of the tools you see on both the Penn State test and main instances. You can also get tools form the tool shed if you want - see our wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed for information about how to do this. I don't think you'll need to use the tools_fabfile script from mi_deployment repo for your local instance.
Also, if I have problems with this server sending out emails (which may be the case) am I going to run into trouble with user/password management or can I just admin everything manually? There will only be a very small number of users on this server.
I'm not clear on this question, but you certainly shouldn't run into any problems with user / password management within Galaxy. From the Galaxy Admin interface you have the ability to "Manage users" where you can reset passwords if necessary.
If I have missed any good 'getting started' documentation on config/admin of a local install please point me in the right direction. I've been looking at http://wiki.g2.bx.psu.edu/Admin .
You found the right wiki.
Thanks, Clare
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759
___________________________________________________________ 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:
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759
participants (3)
-
Clare Sloggett -
Enis Afgan -
Greg Von Kuster