Birkbeck Biocomputing II Skeleton Code

This provides some skeleton code for demonstrating how the three-layer model works for the Biocomputing II project.

Most importantly, it provides the required way in which files are expected to be laid out in the GitHib submission.

A good place to start would be to try this out.

1. Create a file called config.sh using one of the config_xxxx.sh files as a template. At Birkbeck, you should just need to do cp config_bbk.sh config.sh. The values of html and cgi are the locations where you need to install your HTML files and CGI scripts.

2. Create a file called cgi-biocomp2/config.py. You can use cgi-biocomp2/config_demo.py as a template. Change cgiURL to point to the path used to access a CGI script in a URL (at Birkbeck, something like /cgi-bin/cgiwrap/ab123/ (where ab123 is replaced by your username).

3. Run the install script by typing ./install.sh

You should now be able to point your browser to the URL of the location in which you stored the HTML.

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How to use this skeleton

1. One member of your team must create a private repository on your GitHub account.

2. Allow the other members of the team read/write access to the repository:

• Click Settings (at the top)
• Click Manage access (on the left)
• Click Invite a collaborator
• Add each of the members of your team

We will assume your GitHub username is JohnSmith and your repository is called BBKProject. Take the following steps:

git clone git@github.com:AndrewCRMartin/biocomp2.git
cd biocomp2
git remote rm origin
git remote add origin git@github.com:JohnSmith/BBKProject.git
git push -u origin master

You have now created your own repository which is a copy of this skeleton project and synchronized it with your own GitHub.

You can now all clone the repository to your own machines or unix accounts and edit the code. Don't forget to commit and push your changes back to GitHub regularly and remember to pull down other people's changes.

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The code is organized into three main directories:

• createdb This is where the code will live to parse the Genbank file and create the database

• html This is where the HTML files live. If there is an alternative web front end then this would be in an html2 directory

• cgi-biocomp2 This is where the CGI scripts and all the code for the different layers lives.

The cgi-biocomp2 directory contains three sub-directories that represent the three layers of code:

• cgi-biocomp2/cgi contains the CGI scripts. If there is an alternative web front end then this would be in an directory called cgi-biocomp2/cgi2

• cgi-biocomp2/bl contains the business layer code.

• cgi-biocomp2/db contains the database access layer code.

The install.sh script in the top directory is a demonstration script that will copy the files to HTML and cgi-bin directories. See the instructions above for using these on the server at Birkbeck.