Clotho Installer - Requirements

[maxbates]

• MongoDB
  • It needs to install the database
  • Ideally the path to the database is passed to Clotho such that it can clear the lock file
  • The database needs an initial population with some Sharables
  • It needs to check for preinstalled MongoDB, and respond appropriately
  • starting the mongo process at clotho startup, and shutting it down on exit
• Python and BioPython
  • It needs to install both of these packages
  • It needs to put the path link into the system registry such that 'python' can be invoked
  • It needs to check for preinstalled python, and respond appropriately
• Settings
  • It needs to ask the administrator about whether this instance of Clotho should present a public webserver
  • Ask whether it should ever export public data
  • Probably a bunch of other questions. All settings should default to something reasonable, but admin has the option of changing them.
• Presenting the webservice
  • Push whatever magic buttons make the public server go live

[PrashantVaidyanathan]

Top Level Overview: I was thinking it would be a good idea to have 3 separate requirements/strategies for each operating System. Hence for each operating system we would have the following: 1) Minimum System requirements 2) Check if the dependencies have been installed 3) Executable: and what happens when you click on them. Do we need to store local data and log files? If so where will they be stored?

As for the operating Systems: 1) Ubuntu/Linux operating systems. This should be fairly straightforward. I could create a package installer that simply unpacks the dependencies, and creates an executable. Launching the exe should start mongoDB and launch Clotho.

2) Windows: a) Do we give the user a choice as to where they would like the Dependencies will be installed? b) It should ask where the user would like to store local data. c) We could probably have Custom/Express install options for this. So Custom install can be used by experienced users. Launching the exe should start mongoDB and launch Clotho.

3) Mac OS Sadly I dont have a lot of experience using a Mac. So I'll have to look into this a little more before I comment on this.

[jcaucb]

2) Windows: a) Do we give the user a choice as to where they would like the Dependencies will be installed?

Yes, giving options is good, but they should all default to something typical. Very few users will understand what's going on here enough to tell you where to put things.

b) It should ask where the user would like to store local data.

Except for the database, I'm not so sure there is any local data.

c) We could probably have Custom/Express install options for this. So Custom install can be used by experienced users.

Alternatively, you give experienced users the build instructions.

[PrashantVaidyanathan]

Just to bring in Kelvin's note regarding Python. It would seem that the best option is to install a copy of Python (even if it is a duplicate one). Advanced users can have the option to not install Python. Perhaps we could just have a separate warning note asking users to provide the path to Python (perhaps this can be incorporated within the installer's flow)

[jcaucb]

yes, sounds good

On Thu, May 22, 2014 at 12:55 PM, Prashant Vaidyanathan < notifications@github.com> wrote:

Just to bring in Kelvin's note regarding Python. It would seem that the best option is to install a copy of Python (even if it is a duplicate one). Advanced users can have the option to not install Python. Perhaps we could just have a separate warning note asking users to provide the path to Python (perhaps this can be incorporated within the installer's flow)

— Reply to this email directly or view it on GitHubhttps://github.com/CIDARLAB/clotho3/issues/305#issuecomment-43936282 .

J. Christopher Anderson, Ph.D. Assistant Professor Department of Bioengineering http://andersonlab.qb3.berkeley.edu/

Office: 512E Energy Biosciences Building (EBB) Lab: 5th Floor EBB

Mailing Address: J. Christopher Anderson University of California, Berkeley 512E Energy Biosciences Building Berkeley, CA 94720

[PrashantVaidyanathan]

Optional Dependencies:

In the Build instructions in the Wiki page, building the front-end is optional. Is this specific for the dev-environment? If not, should the installer have an option letting the user install dependencies required for the front end, like Node.js, Bower, Grunt and Compass?

[jcaucb]

The node.js/bower/grunt thing is all for Max to develop the client-code. That is not something that should be included for an install by a bio-user.

On Fri, May 23, 2014 at 1:42 PM, Prashant Vaidyanathan < notifications@github.com> wrote:

Optional Dependencies:

In the Build instructions in the Wiki page, building the front-end is optional. Is this specific for the dev-environment? If not, should the installer have an option letting the user install dependencies required for the front end, like Node.js, Bower, Grunt and Compass?

— Reply to this email directly or view it on GitHubhttps://github.com/CIDARLAB/clotho3/issues/305#issuecomment-44058001 .

J. Christopher Anderson, Ph.D. Assistant Professor Department of Bioengineering http://andersonlab.qb3.berkeley.edu/

Office: 512E Energy Biosciences Building (EBB) Lab: 5th Floor EBB

Mailing Address: J. Christopher Anderson University of California, Berkeley 512E Energy Biosciences Building Berkeley, CA 94720

[maxbates]

is this still in use / relevant?

[PrashantVaidyanathan]

It is still relavant. I'll move this to the Installer milestone and mark it complete when the Installer is done.

[PrashantVaidyanathan]

492 is the way to go for this. No more installers.