== README

This is OperaHouse webface which allows users to run our lab's computational-heavy tools using web form. Our lab is specialized on sequence and motif analysis so our tools have some stuff to simplifing this kind of tasks.

In order to setup opera house you'd check several points:

* Place motif collections onto their place in `public/motif_collections/` folder.
Each of subfolders pcm/pwm/thresholds/logo have its own subsubfolders: hocomoco/homer/swissregulon/jaspar/selex. These collection-specific folders should contain motifs in plain text formats (extensions: .pcm/.pwm/.ppm) or motif specific information: (.thr/_direct.png/_revcomp.png). Make sure that no other files are in these folders (no `.keep` files, they break tools)

* Check for the latest versions of Java-tools (`scan-collection.jar`, `multi-SNP-scan.jar`). They should be placed in public folder.

In order to run webface do:

* `cd path_to_app && bundle install`

* `echo "cd path_to_app && source path_to_ruby_dir && rvm use 2.0 do bundle exec rails s -e production -p 80 -d" | sudo bash -i`

This command can be scheduled with root's `sudo crontab -e`. It'd be runned under root if you want to use port 80.

* If you change overture files - restart not only webface but also opera house itself (it will be restarted automatically by webface)

# README

This is OperaHouse webface which allows users to run our lab's computational-heavy tools using web form. Our lab is specialized on sequence and motif analysis so our tools have some stuff to simplifing this kind of tasks.

## Setup
In order to setup opera house you'd check several points:

* Place motif collections onto their place in `public/motif_collections/` folder.
Each of subfolders pcm/pwm/thresholds/logo have its own subsubfolders: hocomoco/homer/swissregulon/jaspar/selex. These collection-specific folders should contain motifs in plain text formats (extensions: .pcm/.pwm/.ppm) or motif specific information: (.thr/_direct.png/_revcomp.png). Make sure that no other files are in these folders (no `.keep` files, they break tools)

* Check for the latest versions of Java-tools (`scan-collection.jar`, `multi-SNP-scan.jar`). They should be placed in public folder.

## Run and restart
In order to run webface do:

* `cd path_to_app && bundle install`

* `echo "cd path_to_app && source path_to_ruby_dir && rvm use 2.0 do bundle exec rails s -e production -p 80 -d" | sudo bash -i`

This command can be scheduled with root's `sudo crontab -e`. It'd be runned under root if you want to use port 80.

* If you change overture files - restart not only webface but also opera house itself (it will be restarted automatically by webface)

Update Readme in order to be valid markdown
Update Readme in order to be valid markdown