On Twitter and Collab

[Raoul B.]

Dear All,
I did a post on Twitter about your work #Mirmaid, so ... cool.

It fits wery well with the BioHckathon I'll attand in Tokyo 6-13 Feb
2010.

Pst night I tried to install Mirmaid on Windows 7, some problem with
ferret and rake to fix...

I want to develop the plugin for targetscan (ref private email sent
some days ago), are you interested?

[Morten Lindow]

Dear Raoul

Great to hear that you like miRMaid!

Would be excellent with a targetscan plugin. Go ahead! I suggest you
put it on github. When you want help, discussion or testing just use
the maillist.

Would also be awsome if you could make other bioruby developers
interested

Cheers

Morten

Sent from my iPod

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[Anders Jacobsen]

Hi Raoul,

A target-prediction plugin is really what miRMaid needs most right
now!!

I suggest that you take a look at the miR2Disease plugin code on
github (http://github.com/andersjacobsen/mirmaid_mir2disease), if you
did not already do this ;-)

I think the following is a good way to setup up a plugin development
enviroment:

* After setting up miRMaid locally, create a new directory for the
plugin in vendor/ (i.e. 'vendor/mirmaid-targetscan'). This directory
holds all code for the plugin, so it can be put under version control
on i.e. github.
* start developing the plugin in this directory. I guess one could
start from scratch by iteratively adding unit-tests, features and
implementing code, or by taking an existing plugin and gradually
modifying it towards the goal.

The plugin "API" as it stands now is more proof-of-concept. It can
definetely be improved in a number of ways. I have started a "plugin
development" thread in this group where we can discuss bugs/issues
that you may encounter. Another important aspect for the future is
that plugins/engines in Rails3 are going to be a lot more powerful and
flexible (http://www.engineyard.com/blog/2010/rails-and-merb-merge-
plugin-api-part-3-of-6/, http://www.engineyard.com/blog/2010/rails-and-merb-merge-rails-core-part-4-of-6/).

Finally, we should soon have a little tutorial on plugin development
on the wiki (http://mirmaid.org/doku.php?
id=plugins#how_can_i_implement_my_own_plugin). Raoul, you are very
welcome to contribute to the wiki!

### miRMaid on Windows:
We have not tested this setup. Ferret will only be the first hurdle.
The miRMaid data setup process uses a few standard "Unix" commands
such as 'wget'. This functionality could "in principle" be implemented
in pure ruby so that it would run in Windows. However, for now I think
it is a better strategy to use Linux in a virtual machine on a Windows
computer (I use miRMaid + Windows7 + Ubuntu in Sun's open source
VirtualBox, www.virtualbox.org).

-Anders

[Raoul B.]

On 1 Feb, 12:45, Anders Jacobsen <anders...@gmail.com> wrote:
> ### miRMaid on Windows:
> We have not tested this setup. Ferret will only be the first hurdle.
> The miRMaid data setup process uses a few standard "Unix" commands
> such as 'wget'. This functionality could "in principle" be implemented
> in pure ruby so that it would run in Windows. However, for now I think
> it is a better strategy to use Linux in a virtual machine on a Windows
> computer (I use miRMaid + Windows7 + Ubuntu in Sun's open source
> VirtualBox,www.virtualbox.org).

My config is
Host:W7
Guest: ArchLinux x86

I did the installation procedure and I have problem on line #200 of
lib/tasks/mirmaid.rake, so I commented the "or raise". I can't figure
out the problem.
However commenting the raise, everything goes well.

[Anders Jacobsen]

Hi Raoul,

Ok, I guess this command fails (line 200):

   sqlite3 -init #{mirbase_data_dir}/sqlite_tables.sql #{database} '.exit'

In the rails application root could you try the following shell command:

   sqlite3 -init tmp/mirbase_data/sqlite_tables.sql production  '.exit'

Which version of sqlite3 are you using?

Are you sure everything works when you have commented out the "or raise ..."?

Are you sure all unit tests pass with 'rake mirmaid:test:all' (0 failures/errors)?

-Anders

[Raoul B.]

Hi Anders,

On 3 Feb, 19:56, Anders Jacobsen <anders...@gmail.com> wrote:

> Which version of sqlite3 are you using?
> Are you sure everything works when you have commented out the "or raise
> ..."?
> Are you sure all unit tests pass with 'rake mirmaid:test:all' (0
> failures/errors)?

I switched to Ubuntu 9.10 and now everthing is working out of the box.
I'll use this config.

Thanks.