GoogleAppEngine :: Ubuntu 12.10

Download Google App Engine.

URL: https://developers.google.com/appengine/downloads

Download: google_appengine_1.7.3.zip

Unzip and move it.

$ cd ~/Desktop/

$ unzip google_appengine_1.7.3.zip

google_appengine/*

Check the command

$ ./dev_appserver.py

Create the required files.

$ cd ~/Desktop

$ mkdir helloworld

$ cd helloworld

$ touch helloworld.py app.yaml

$ cat helloworld.py 

print 'Content-Type: text/plain'

print ''

print 'Hello, world!'

$ cat app.yaml 

application: helloworld

version: 1

runtime: python

api_version: 1

handlers:

- uri: /.*

  script: helloworld.py

Run the Application

$ cd ..

$ ~/path/google_appengine/dev_appserver.py helloworld

Visit the browser:

localhost:8080

Its all working good.

To use sqlite instead of MySQL

$ ~/google_appengine/dev_appserver.py --use_sqlite helloworld

Google App Engine :: Mac OS

Download & Install

URL: https://developers.google.com/appengine/downloads

> Download the Google App Engine SDK

> GoogleAppEngineLauncher-1.7.3.dmg

> Double-click on dmg file to install.

Following tutorials at 

https://developers.google.com/appengine/docs/python/gettingstarted/

Created the folder

$ mkdir /path/to/tutorials/helloworld
$ cd /path/to/tutorials/helloworld
$ touch app.yaml helloworld.py

Contents of helloworld.py

print 'Content-Type: text/plain'

print ''

print 'Hello World'

Contents of app.yaml

application: helloworld

version: 1

runtime: python

api_version: 1

handlers:

- url: /.*

  script: helloworld.py

Start Google App Engine.

File > Add Existing Application > helloworld > open > Run

ERROR:

*** Running dev_appserver with the following flags:

    --admin_console_server= --port=8080

Python command: /usr/bin/python

WARNING  2012-12-04 16:23:33,337 rdbms_mysqldb.py:74] The rdbms API is not available because the MySQLdb library could not be loaded.

Checking Python version

$ which python

/Library/Frameworks/Python.framework/Versions/2.7/bin/python

$ python --version

Python 2.7

Checking for MySQL

$ mysqladmin -u root -p status

Enter password: 

Uptime: 2627  Threads: 1  Questions: 3  Slow queries: 0  Opens: 33  Flush tables: 1  Open tables: 26  Queries per second avg: 0.001

If you have already install Macports

$ sudo port install py26-mysql

Else, Install Macports

url: https://distfiles.macports.org/MacPorts/

download: MacPorts-2.1.2.tar.gz

On terminal

$ tar zxvf MacPorts-2.1.2.tar.gz

$ cd MacPorts-2.1.2

$ ./configure

$ make

$ sudo make install

/opt/local/bin should be added to my $PATH

$ vim ~/.bashrc

export PATH=$PATH:/opt/local/bin

$ source ~/.bashrc

$ sudo port -v selfupdate

$ sudo port search python | grep mysql

$ sudo port install py26-mysql

Using Macports didnot solve my problem.

So I will use the MySQL-python binaries.

URL: http://sourceforge.net/projects/mysql-python/

Download: MySQL-python-1.2.4b4.tar.gz

Terminal:

$ tar zxvf MySQL-python-1.2.4b4.tar.gz

$ cd MySQL-python-1.2.4b4

$ vim site.cfg

## Comment this line

#mysql_config = /usr/local/bin/mysql_config

## provide path to mysql_config

mysql_config = /usr/local/mysql/bin/mysql_config

$ python setup.py build

$ sudo python setup.py install

Looks good so far. Check if everything works

$ python

Python 2.7 (r27:82508, Jul  3 2010, 21:12:11) 

[GCC 4.0.1 (Apple Inc. build 5493)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import MySQLdb

>>> 

Rerun the Google App Engine.

I was not able to solve the problem. The ERROR message still stays the same.

__END__

VIM :: remove lines :: pattern

- To remove lines in a file which matches a pattern
- Open file using VIM
$ vim filename.txt

- To remove lines that has "food101" in it
:g/.*food101.*/d

Phred :: Install

Phred

The installation is in the server
working directory: /bioinfo/packages/Phred

Copy the phred-dist-020425.c-acd.tar.Z to above directory
$ uncompress phred-dist-020425.c-acd.tar.Z
$ tar xvf phred-dist-020425.c-acd.tar

Edit makefile to uncomment lines for 'UNIX specific definitions'
$ make

To set the environment variable
$ export PHRED_PARAMETER_FILE=\usr\local\etc\PhredPar\phredpar.dat

== Now ready to run phred

phd2fasta package
move the package to the working directory
$ uncompress phd2fasta-acd-dist.tar.Z
$ tar xvf phd2fasta-acd-dist.tar
$ make

The program can be executed as ./phd2fasta