The most common frame work Django offers great features for web-programming with python.

I have to take care of pip installation on my mac

easy_install is the way to go, yeh.

Here is another help link for django web-development

It is not surprising that nothing will work as simple as it seems. Well, here the first verification failed:

python manage.py runserver

generates

maximum recursion depth exceeded

Someone kindly posted answer. Well, my functools.py is empty.

The answer is “python” had bugs (working with django), so upgrading python installation solved the problem.

Using MySQL in Django

My database is mysql, so I was tying to incorporate MySQL for django. As usual, nothing works as I expected. When I ran python manage migrate, I got error

….
  File "/Library/Python/2.7/site-packages/django/db/backends/mysql/base.py", line 28, in 
    raise ImproperlyConfigured("Error loading MySQLdb module: %s" % e)
django.core.exceptions.ImproperlyConfigured: Error loading MySQLdb module: No module named MySQLdb
….

So, the problem was the “MySQLdb” module as someone pointed out. Well, again the installation itself reached error

RuntimeError: maximum recursion depth exceeded
/Users/li11/django/mysql/MySQL-python-1.2.4b4/distribute-0.6.28-py2.7.egg
Traceback (most recent call last):
  File "setup.py", line 7, in 
    use_setuptools()
  File "/Users/li11/django/mysql/MySQL-python-1.2.4b4/distribute_setup.py", line 145, in use_setuptools
    return _do_download(version, download_base, to_dir, download_delay)
  File "/Users/li11/django/mysql/MySQL-python-1.2.4b4/distribute_setup.py", line 125, in _do_download
    _build_egg(egg, tarball, to_dir)
  File "/Users/li11/django/mysql/MySQL-python-1.2.4b4/distribute_setup.py", line 116, in _build_egg
    raise IOError('Could not build the egg.')
IOError: Could not build the egg.

Using PostgreSQL in Django

It turns out that hooking up django with mysql is not that easy, I have got help from Andy who gave me their project on github repository. Well, they sticked with postgresql version 9.4+.

My mac has 9.0, so I have to upgrade it to 9.4+. It seems that postgres.app provides the easiest solution to mac user.

Next, I need to set path for postgresql

Using the Python virtualenv and virtualenvwrapper

Andy’s project needs these prerequisite, and I found this help doc for virtual environment.

Missing llvm-gcc-4.2 on Mac OS

My configuration failed at

pip install -r requirements/dev.txt

With the following error message

    llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -DPSYCOPG_DEFAULT_PYDATETIME=1 -DPSYCOPG_VERSION="2.5.5 (dt dec pq3 ext)" -DPSYCOPG_EXTENSIONS=1 -DPSYCOPG_NEW_BOOLEAN=1 -DHAVE_PQFREEMEM=1 -DPG_VERSION_HEX=0x09000D -DPSYCOPG_EXTENSIONS=1 -DPSYCOPG_NEW_BOOLEAN=1 -DHAVE_PQFREEMEM=1 -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I. -I/usr/include -I/usr/include/postgresql/server -c psycopg/psycopgmodule.c -o build/temp.macosx-10.7-intel-2.7/psycopg/psycopgmodule.o
    unable to execute llvm-gcc-4.2: No such file or directory
    error: command 'llvm-gcc-4.2' failed with exit status 1

Found a bunch of posting. After upgrading ox-10.11, all works out just fine.

People reported same errors
This one needs compiling from github source
Apple Store is the best answer

I found this website by Marina, I would like to follow this note and get the speed up on python and python web.

Note 1: 2/12/2016

Today,I was looking at the SNP association analysis. I found this write up by Eric Minikel is very helpful.

Matti Pirinen from Finland has a good website also.

This is an embarrassed note as I could not download miRBase using ftp. Hopefully, I can figure it out somehow and keep a note for future use.

Scenario I: I wanted to download database files from mirbase ftp server

I was at miRBase download page
Here is the README file
I clicked Go to the FTP site to download al file.
From my linux window, " ftp ftp.mirbase.org/pub/mirbase/21/database_files/" gets me "unknown host" error
What did I do wrong??

Well, the fix is simple, the serve name was only mirbase.org haha

ftp mirbase.org
user: anonymous
pass: li11@niehs.nih.gov
prompt

Frank created a database called miRBaseV21 on the “wine” server

mysql> show grants for li11;
| GRANT ALL PRIVILEGES ON `li11`.* TO ‘li11’@’%’ WITH GRANT OPTION
| GRANT ALL PRIVILEGES ON `mirDB`.* TO ‘li11’@’%’
| GRANT ALL PRIVILEGES ON `methylSNPdb`.* TO ‘li11’@’%’
| GRANT ALL PRIVILEGES ON `miRBaseV21`.* TO ‘li11’@’%’
| GRANT ALL PRIVILEGES ON `mus_musculus_core_73_38`.* TO ‘li11’@’%’

Scenario II: I need to create the schema downloaded from mirbase.

It turns out that "mysqldump" does not work following my earlier post, it could be that I do NOT have root privillege
Followed this link, I used "mysql> source ~/mysql_jyl/miRBase/miRBaseV21/tables.sql" ; 

In the end, I imported all the data into the database:

mysql> load data local infile ‘~/mysql_jyl/miRBase/miRBaseV21/wikipedia.txt’ into table wikipedia ;

Now, I am working on R scripts for the analytical components. At first, I have to work on connecting to the mysql database. Here are a few lines of code to connect:

library(RMySQL)
mydb = dbConnect(MySQL(), user='li11', password='password', dbname='mirDB', host='wine.niehs.nih.gov')
dbListTables(mydb)
dbListFields(mydb, 'resCenter')

It turns out that it is quite simple and straightforward with the following help links:

Main link at R-blogger
A brief tutorial post by Manoj Kumar

To transfer my RATEmiRs from wine to my windows machine, here are a few simple steps:

1. On linux, do the mysqldump: mysqldump -u li11 -ppassword RATEmiRs > ~/RATEMiRs.sql 
2. On windows machine: Log in mysql database and create a database (create database ratemirs)
3. Do a simple restore: mysql -u li11 -p ratemirs < x:\RATEMiRs.sql

With the new computer, I could NOT find the “MyOwnArchive”.

Through very hard effort, I got it done

	
Go to "File"
	
Choose "Account Settings"
	
Choose "Data Files"
	
Choose "Add..."
	
Choose default location "MyOwnArchive.pst"

It turns out, this “MyOwnArchive.pst” has been backed up by the server and all my “local” folders are recovered. Therefore, I decided to document this with a successful screenshot.