setting up computer to run program 9-23-12

2014-08-29

azim58 - setting up computer to run program 9-23-12

First Cygwin needs to be installed. When installing cygwin, make sure
that the Development package is installed (it may not be set to be
installed by default). This package allows you to run the "make" command
to install and compile other programs later. Make sure that ssh also gets
installed (installing ssh onto cygwin)
Cygwin then needs to be setup so that it can be called from the regular
command line. Something like C:\cygwin\bin needs to be added to the
environment variable path. See environment variable path

Then glam2 needs to be installed with cygwin. Installing glam2. This
action actually installs glam2scan as well as glam2. The glam2 src file
can be added to the Windows environment variable path so that glam2 can
be called from any directory.

Install Blast. Blast can be downloaded here:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
All of the databases for blast can be updated with this command
./update_blastdb.pl htgs
as seen here
http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.3_Quick_start
or individual databases can be installed
ftp://ftp.ncbi.nlm.nih.gov/blast/db/
For example, one might just want to download the nr database for the
non-redundant sequences. Extract the database. Then blast can be called
from the command line like this.
blastp -db nr.00 -query test_fasta.fsa -out results.out
You may need to put a ./ in front of the blastp part.
The Blast directory can then be added to the windows environment variable
path.

Get Bepipred up and working. Install VirtualBox and a Linux operating
system if these things aren't already installed. Install bepipred onto
the Linux system. Commands can be issued to the linux system from the
windows host command line. To do this the virtual box network adapter has
to be set to a host only adapter or bridged adapter (bridged adapter
seems to be better because it allows the internet on the linux machine to
work as well). Then you need to determine the ip address on the machine
by typing ifconfig at a terminal (CTRL+ALT+T opens a terminal in Linux).
Make sure that the openssh-server is installed on the linux virtualbox by
typing "sudo apt-get install openssh-server" at a command line. Then the
virtual box can be controlled from windows with the following command:
ssh username@ipaddress (e.g. ssh kurt@192.168.56.101). Install the tcsh
shell with the terminal command "sudo apt-get install tcsh". Follow the
directions in the bepipred readme file to get everything up and running.
Note that the sticky bit can be checked as follows.
ls -ld /tmp
this gives a result like
drwxrwxrwt+ 1 kwhittem Domain Users 0 Sep 23 11:57 /tmp
the sticky bit is represented by the letter t in the final character-place
Bepipred can then be run with a command like
./bepipred test/CHO.fsa
A file can be written like this
./bepipred test/CHO.fsa >output.txt
The ssh connection can be ended by typing exit
Files can be copied from the remote machine to the current one like this
scp kurt@10.212.30.30:/home/kurt/bepipred-1.0b/out.txt
/home/kwhittem/test/out.txt

Next setup up a new project in Eclipse with all of the classes that you
need. The classes can be found here:
C:\kurt\storage\CIM Research Folder\DR\2012\9-6-12\Motif Peptide
Analysis\classes

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