Program :: Emboss

Download URL: ftp://emboss.open-bio.org/pub/EMBOSS/

At TALON, 

$ wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.3.1.tar.gz

$ tar zxvf EMBOSS-6.3.1.tar.gz

$ cd EMBOSS-6.3.1

$ ./configure

$ make

$ ./emboss/needle --help

It should now be working

Program :: FASTA

Download url: ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/CURRENT/fasta-36.3.4.tar.gz

$ wget ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/CURRENT/fasta-36.3.4.tar.gz
$ tar zxvf fasta-36.3.4.tar.gz
$ cd fasta-36.3.4


$ cd src/

$ make -f ../make/Makefile.linux_sse2 all

$ cd ..

$ .bin/fasta36 --help

$ /bin/fasta36 -d 10 -E 1e-20 -q input.fasta database.fasta -O fasta.output

CytoscapeWeb :: Instructions.

URL: http://cytoscapeweb.cytoscape.org/


Downloaded version 0.7.2

$ unzip cytoscapeweb_v0.7.2.zip

svn checkout http://chianti.ucsd.edu/svn/cytoscapeweb/trunk cytoscapeweb-all-read-only

Cytoscape :: Plugins :: Download

Plugins > Manage Plugins > Keyword search for plugin

Downloading plugin for Multicolored Node, where each node is divided into pie depending on the attribute. Additional notes is present at http://groups.google.com/group/cytoscape-discuss/browse_thread/thread/12ccc21ae5756778

To download and install a plugin
Go to

$ cd ~/Cytoscape_v2.8.1/plugins
$ wget http://url.to.site/multicolor

Restart Cytoscape to include it in Cytoscape.

A rainbow wheel named color nodes should appear on top of the window.

Intersting Plugins:
Venn Diagram: http://www.dishevelled.org/venn-cytoscape-plugin/
User-defined: http://www.genmapp.org/BubbleRouter/manual.htm

Qiime : Install : HPC

on TALON,
check if python is available

$ what python
/usr/bin/python

Installing Dependencies required for all features of Qiime.
1. Numpy 1.3.0
Source: http://sourceforge.net/projects/numpy/files/NumPy/1.3.0/numpy-1.3.0.tar.gz/download
Dependencies:
1.A. Nose

$ wget http://somethingaboutorange.com/mrl/projects/nose/nose-1.0.0.tar.gz
$ tar zxvf nose-1.0.0.tar.gz 
$ python setup.py install --prefix=$HOME/bin/python

Edit ~/.bashrc and enter the line below

export PYTHONPATH=$PYTHONPATH:$HOME/bin/python

Refresh bash, and check the installation of Nose

$ source ~/.bashrc
$ python -c "import nose"

Untar and install Numpy

$ tar zxvf numpy-1.3.0.tar.gz
$ cd numpy-1.3.0

Download PyCogent-1.5 from http://sourceforge.net/projects/pycogent/files/PyCogent/1.5/PyCogent-1.5.tgz/download
Unpacking and Installing

$ tar zxvf PyCogent-1.5.tgz
$ cd PyCogent-1.5

what