How to convert PatentIn Sequence listing file back to FASTA

I wrote this up as a wiki on my github site. Click the link to visit.

-Mark

Problems starting MySQL

Using MySQL 14.14 distrib 5.7.9 for osx10.11 on El Capitan 10.11.3

An existing MySQL database suddenly stopped running after a restart. When I tried to connect I first got this error:

Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

So tried to run mysql.server start and got this error:

ERROR! The server quit without updating PID file (/usr/local/var/mysql/Honshu.local.pid)

Tried using sudo but that did not change anything.

Went to install location and removed the *.err file (which was 53Mb!?)

sudo rm /usr/local/var/mysql/Honshu.local.err

Then ran mysql.server start and it started up just fine.

How to Install Shiny Server on OSX

I want to set up the shiny-server to run on an iMac at work so that we can run multiple R-apps over the intranet. According to the docs for Shiny server, OSX is not supported yet (version 1.1.0) so we are going to build it from source and hope for the best!

Instructions for building from source are here. We follow them pretty closely but there are a few gotchas.

The full HowTo is on our GitHub Wiki, here

Creating a Mountain Lion development environment

So I had to set up a new dev environment at work on Mountain Lion. It uses the following components

• Hombrew
• Python 2.7.5
• Django 1.5.2
• Apache 2.2.25
• Postgres 9.2.4
• R 3.0.1
• Virtualenv

and a bunch of other python libraries and stuff. This system is set up for Bioinformatics development, so there are things that are specific to that. The build is documented on our internal wiki, but I copied the build instructions to the *new* code.ex(python) wiki in my personal github account. The direct link to the build instructions is here.

Understanding Django static files

In struggling to setup a new development/production server on Mountain Lion, I came across this good explanation of django static files and how to configure them.

http://bitsoul.com/2012/10/04/understanding-django-static-files-for-beginners/

Also, this link was also helpful in setting up the environment

http://thecodeship.com/deployment/deploy-django-apache-virtualenv-and-mod_wsgi/

Cheers.

Zipping a python dict of lists

Have a python dictionary containing lists. Want to zip the lists together, but don't know the keys. Solution provided from Stackoverflow

http://stackoverflow.com/questions/9828072/zipping-a-python-dict-of-lists

How to install mod_wsgi on Mountain Lion

There are apparently changes Apple made in XCode between Lion and Mountain Lion that cause the standard install method to fail. The conventional fix that comes up most often in a Google search at the time of this writing is to create a symlink between the new name of a Toolchain folder and the old name that the installer is supposedly looking for, like this 

sudo ln -s /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/ /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain 

I did this and tried to make mod_wsgi using Homebrew but it throws a cryptic apxs error. Long story short, I eventually compiled mod_wsgi from source myself, but it continued to through various errors, even though things seemed to be configured properly. I went back to a different Mountain Lion machine I had configured earlier using MacPorts. When I did that machine, I had no problems with mod_wsgi or the need for this toolchain symlink. Examining the Portfile for mod_wsgi gives the key. The missing element is adding the --disable-framework flag to the config file. After that, everything works fine. 

This flag should be added to the Homebrew Formula for mod_wsgi. I have never made a Formula before, but maybe one day I will do it. Below is the Gist showing what I did and how it worked.