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