Display database specific information on each sequence server instance,

Hi Anurag, Cedric, Yannick, Ben

Thank you all for keeping good work up related to sequence server. Our research community is getting benefited by your efforts.

I have installed sequence server on my CentOS 6.2 server using gem install sequenceserver successfully and everything is fine.

I have further configured sequence sever to host 5 different virtual hosts for 5 different private datasets by integrating SS with Apache and incorporating Virtualhost directives in httpd.conf file

However I need to display some database specific information on each SS page for the awareness of users,

For e.g. if someone access wheat related ss then on ss page that opens I want to display wheat related information and the same is true for other databases also.

But if I made any change in search.erb file then it will display in all ss instances irrespective of which genomic database that ss instance is hosting.

Kindly suggest how can I display some basic database specific information on each ss instance.

It's a little bit of a work, but you can have a different search.erb
driving each virtual host -- just like you have 5 different config
file at the moment.

-- Priyam

Thanks priyam for your prompt reply,

At least I am assure now that it can be done,

kindly tell how should i go about making new search.erb and putting it under specific SS,

or if I can copy and paste the old search.erb by making some desirable changes, and where should i put the new seacrh.erb file,


$ gem install sequenceserver
$ sequenceserver
Created a dummy config file at ~/.sequenceserver.conf

For each instance:

$ mkdir -p ss_bees/tmp
$ cp ~/.sequenceserver.conf ss_bees
$ cp /path/to/ss/config.ru ss_bees
$ cp -r /path/to/ss/public ss_bees

... edit search.erb, etc to your liking ...

$ less config.ru

require 'rubygems'
require 'sequenceserver'

## for each instance tell SS we are not following conventions
SequenceServer.config_file = /absolute/path/to/config_file
SequenceServer.public_dir = /absolute/path/to/public/dir

Hi priyam,

Thank you for responding timely,

As you suggested I have already made 5 different directories one for each ss and I added SequenceServer.public_dir=’‘absolute/path/to/public/dir’ but I ran into errors

I tried what you suggested but I am running through following errors , I am posting the exact syntax of error as given by phusion passenger on apache

O.K. I dig up on google and replaced public_dir with public_folder and this time there were no error relate to undefined method and the sequenceserver page also displayed properly.

But still the changes that i made to search.erb file are not displayed on ss page the ss is till using the source ss views,

Priyam if you don’t mind please correct me if I am wrong , you told me to use public_dir/public_folder* but public folder is keeping the design related files i.e css, js and image folders inside it but it seems that the page that is displayed on typing SS url is the one present inside views folder under SS installation directory i.e “search.erb” so should we be not looking for something similar to views_dir/view_folder in config.ru instead of public_dir because search.erb file is present inside views folder and i changed search.erb not the css/img/js files,

Kindly tell how can I rsolve this issue of displaying database specific information on each virtual host ss instance.

Thanks for going through my post.

O.k. Hi again!!! Priyam,

This time I finally went through and everything is working like harm!!!

It seems that I was indeed right on adding SequenceServer::App.views = ‘path/to/changed/search.erb/file’ inside config.ru in place of public_dir and I again do some hit-and-trial by changing the config.ru file each time with different syntax for adding views because I am not a ruby/rack expert so I resort to hit and trial approach and it finally worked for following syntax

Add in config.ru

SequenceServer::App.views = ‘/path/to/customised/search.erb/file’

that’s it, I finally got it.

Thanks Priyam and sequenceserver team for your help and support in this matter.

My bad. Right, it's App.views for search.erb. And App.public /
App.public_folder (not sure) if you want to change css, js, etc.

I hope this thread helps others too.


-- Priyam