Git :: Install :: Setup

Install GUI
$ sudo apt-get install git-core gitk git-gui

URL: http://www.digitalmediaminute.com/article/3264/git-tutorial

To create a repository
$ cd testGit
$ git init

This is to setup the configuration to contain ur name and email
This will be used to give information on who committed
$ git config --global user.name "Kashi Revanna"
$ git config --global user.email "Kashi.Revanna@unt.edu"

So now create a file and a directory
$ touch file1
$ mkdir dir
$ git commit

Now to check git, open the file and enter a line
$ git diff
- will list the lines which are different from the ones in the repository

To add a file to the repository
$ touch file2
$ mkdir dir1
$ git add file2
$ git add dir1
$ git commit -m "Add files"

Observe the log files created
$ git log
$ git log -n3
$ git log --stat --summary
$ git log -p

For GUI,
$ gitk

R :: Install :: ClassComparison :: ClassDiscovery

Install R

$ sudo apt-get install r-base

$ sudo apt-get install r-base-dev r-base-core

Go to R

$ sudo R

> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)

- ran into warnings and errors

- Error : package 'Biobase' could not be loaded

- Information to install biobase, http://www.bioconductor.org/packages/2.2/bioc/html/Biobase.html

> source("http://bioconductor.org/biocLite.R")
> biocLite("Biobase")
> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)

- select ClassComparison

- you should get the following sentence

* DONE (ClassComparison)

check if the package is installed
> library('ClassComparison')

> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)
- select ClassDiscovery

- Error : package 'mclust' could not be loaded

To install mclust

> install.packages("Rserve")

* Done (Rserve)

On unix:
$ wget http://bioconductor.org/packages/1.9/bioc/src/contrib/vsn_1.12.0.tar.gz

$ sudo R CMD INSTALL vsn_1.12.0.tar.gz

* Done (vsn)

Go to R

$ sudo R

> install.packages('mclust')

* Done (mclust)

> install.packages(repos="http://bioinformatics.mdanderson.org/OOMPA", dependencies=TRUE)

 * DONE (ClassDiscovery)

check installation
> library('ClassDiscovery')

Ubuntu :: Sort :: Numbers and Alphabets

$ sort -n characters
a
about
1
3
5
12
33
44

Install :: ClustalW :: Local

Download the ClustalW source code from 
ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.12/


$ wget ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.12/clustalw-2.0.12.tar.gz
$ tar zxvf clustalw-2.0.12.tar.gz 

$ cd clustalw-2.0.12

$ ./configure 

$ make
If you have sudo access, run 'make install', else use clustalw2 in the src directory.

$ cd src/

$ ./clustalw2

 **************************************************************

 ******** CLUSTAL 2.0.12 Multiple Sequence Alignments  ********

 **************************************************************

     1. Sequence Input From Disc

     2. Multiple Alignments

     3. Profile / Structure Alignments

     4. Phylogenetic trees

     S. Execute a system command

     H. HELP

     X. EXIT (leave program)

Your choice: X

Now run the clustalW

Ruby :: Pie :: SVG :: Graph

Download SVG from http://www.germane-software.com/software/SVG/SVG::Graph/

Place the SVG folder in the current folder

=====

require 'SVG/Graph/Pie'

fields = %w(Staphylococcus Corynebacterium Acinetobacter Propionibacterium Rothia Pseudomonas Leptotrichia Herbaspirillum Stenotrophomonas Streptococcus)

dataVal = [0.46494, 0.43779, 0.02067, 0.01934, 0.01081, 0.00155, 0.00109, 0.00105, 0.00027, 0.00014]

graph = SVG::Graph::Pie.new({:height => 400, :width => 800, :fields => fields })
graph.add_data({
    :data => dataVal,
    :title => 'TITLE',
})

graph.expanded = false
graph.expand_gap = 3
graph.show_data_labels = true
graph.show_key_data_labels = true
graph.show_percent = true
graph.show_shadow = false
graph.datapoint_font_size = 40

output = File.open('test1.svg', "w+")
output.write graph.burn()
output.close

=================================

The file should be written

Another method is to 
 $ sudo gem install gruff

Install :: Treeview

Download

http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html

$ wget http://darwin.zoology.gla.ac.uk/%7Erpage/treeviewx/download/0.5/tv-0.5.1.tar.gz

$ tar zxvf tv-0.5.1.tar.gz

$ cd tv-0.5.1/

$ ./configure

I got an error

configure: error: "Could not find wx-config: is wxWindows installed?"

$ sudo apt-get install libwxgtk2.6-0 libwxgtk2.6-dev libwxgtk2.8-0 libwxgtk2.8-dev

$ ./configure

$ make

Still having problems

charactersblock.cpp: In member function ‘char CharactersBlock::GetState(int, int, int)’:

charactersblock.cpp:1048: error: ‘strlen’ was not declared in this scope

charactersblock.cpp: In member function ‘int CharactersBlock::IsInSymbols(char)’:

charactersblock.cpp:1286: error: ‘strlen’ was not declared in this scope

charactersblock.cpp: In member function ‘virtual void CharactersBlock::HandleFormat(NexusToken&)’:

charactersblock.cpp:1900: error: ‘strcpy’ was not declared in this scope

charactersblock.cpp: In member function ‘int CharactersBlock::PositionInSymbols(char)’:

charactersblock.cpp:3029: error: ‘strlen’ was not declared in this scope

charactersblock.cpp: In member function ‘virtual void CharactersBlock::Report(std::ostream&)’:

charactersblock.cpp:3271: warning: deprecated conversion from string constant to ‘char*’

charactersblock.cpp: In member function ‘void CharactersBlock::ResetSymbols()’:

charactersblock.cpp:3345: error: ‘strcpy’ was not declared in this scope

charactersblock.cpp: In member function ‘void CharactersBlock::WriteStates(DiscreteDatum&, char*, int)’:

charactersblock.cpp:3609: error: ‘strlen’ was not declared in this scope

make[2]: *** [charactersblock.o] Error 1

make[2]: Leaving directory `/home/krevanna/Desktop/tv-0.5.1/ncl-2.0/src'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/home/krevanna/Desktop/tv-0.5.1/ncl-2.0'

make: *** [all-recursive] Error 1

Alternative, get the DRAWTREE program

Download from http://www.daimi.au.dk/~mailund/drawtree.html

$ wget http://www.daimi.au.dk/~mailund/drawtree/drawtree-0.1.3.tar.gz

$ tar zxvf drawtree-0.1.3.tar.gz

$ cd drawtree-0.1.3/

$ drawtree.py -b < ../idealSeqs.AAG.phy.dnadist.neighbor.outtree > mytree.eps

RORails :: Stylesheet

I had a problem with the CSS Stylesheet

Order of events

- file style.css created 

- file is saved in public/stylesheets/ folder

- below line included in layout page.

 <%= stylesheet_link_tag "style", :media => "all" %>

- It worked first time, but then when i refresh the page, 

the error was something like this,

=============================

ERROR NoMethodError: private method `gsub!' called for #
    /usr/lib/ruby/1.8/webrick/htmlutils.rb:16:in `escape'
    /usr/lib/ruby/1.8/webrick/httpresponse.rb:232:in `set_error'
    /home/krevanna/Public/MBAP/vendor/rails/railties/lib/webrick_server.rb:94:in `handle_file'
    /home/krevanna/Public/MBAP/vendor/rails/railties/lib/webrick_server.rb:73:in `service'
    /usr/lib/ruby/1.8/webrick/httpserver.rb:104:in `service'
    /usr/lib/ruby/1.8/webrick/httpserver.rb:65:in `run'
    /usr/lib/ruby/1.8/webrick/server.rb:173:in `start_thread'
    /usr/lib/ruby/1.8/webrick/server.rb:162:in `start'
    /usr/lib/ruby/1.8/webrick/server.rb:162:in `start_thread'
    /usr/lib/ruby/1.8/webrick/server.rb:95:in `start'
    /usr/lib/ruby/1.8/webrick/server.rb:92:in `each'
    /usr/lib/ruby/1.8/webrick/server.rb:92:in `start'
    /usr/lib/ruby/1.8/webrick/server.rb:23:in `start'
    /usr/lib/ruby/1.8/webrick/server.rb:82:in `start'
    /home/krevanna/Public/MBAP/vendor/rails/railties/lib/webrick_server.rb:60:in `dispatch'
    /home/krevanna/Public/MBAP/vendor/rails/railties/lib/commands/servers/webrick.rb:66
    /usr/lib/ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
    /usr/lib/ruby/1.8/rubygems/custom_require.rb:31:in `require'
    /home/krevanna/Public/MBAP/vendor/rails/activesupport/lib/active_support/dependencies.rb:153:in `require'
    /home/krevanna/Public/MBAP/vendor/rails/activesupport/lib/active_support/dependencies.rb:521:in `new_constants_in'
    /home/krevanna/Public/MBAP/vendor/rails/activesupport/lib/active_support/dependencies.rb:153:in `require'
    /home/krevanna/Public/MBAP/vendor/rails/railties/lib/commands/server.rb:49
    /usr/lib/ruby/1.8/rubygems/custom_require.rb:31:in `gem_original_require'
    /usr/lib/ruby/1.8/rubygems/custom_require.rb:31:in `require'
    script/server:3
127.0.0.1 - - [06/Jun/2010:12:57:41 CDT] "GET /stylesheets/style.css?1275762019 HTTP/1.1" 500 343
Referer -> /stylesheets/style.css?1275762019
=================================

- This totally takes of the css from the page.

- there is this number associated after the style.css page i am not sure why is this, and what it means

- I tried changing the setting with the cache, but didnt work

- i am still not sure whats causing this problem.

I think it was something to do with WebBrick, so i changed the server gem to mongrel

$ sudo gem install mongrel

$ ruby script/server mongrel
- now it all worked good for me.