First commit adding environment setup and hw directories

.bash_profile

@@ -0,0 +1,25 @@
+if [ -f /home/share/Modules/global/profile.modules ]
+then
+	. /home/share/Modules/global/profile.modules
+# put your own module loads here
+	module load lsf
+        module load gcc/4.8.1 
+fi
+# .bash_profile
+
+# Get the aliases and functions
+if [ -f ~/.bashrc ]; then
+	. ~/.bashrc
+fi
+
+# User specific environment and startup programs
+
+# Permissions
+umask 0002
+
+PATH=$PATH:$HOME/bin
+# ATM added during October setup
+ANTSPATH=${ANTSPATH:="/home/applications/ANTs/1.9.4/bin/"}
+
+export PATH
+export ANTSPATH

.bashrc

@@ -0,0 +1,31 @@
+case "$0" in
+          -sh|sh|*/sh)	modules_shell=sh ;;
+       -ksh|ksh|*/ksh)	modules_shell=ksh ;;
+       -zsh|zsh|*/zsh)	modules_shell=zsh ;;
+    -bash|bash|*/bash)	modules_shell=bash ;;
+esac
+module() { eval `/home/share/Modules/default/bin/modulecmd $modules_shell $*`; }
+#module() { eval `/bin/modulecmd $modules_shell $*`; }
+# .bashrc
+
+# Source global definitions
+if [ -f /etc/bashrc ]; then
+	. /etc/bashrc
+fi
+
+# Project specific environments
+source ~/.projects
+
+# Permissions
+umask 0002
+
+# User specific aliases and functions
+# Added by Cassian 03/29/2016
+umask g+w 
+alias ls="ls --color=auto"
+# Setup a fancy shell command prompt:
+prompt1="\[\e[0;33m\][\A]\[\e[0m\]" # Display the time in the bash prompt
+prompt2="\[\e[1;39m\]\u@\h:\W\$\[\e[0m\]" # Add username@host:dir$
+promptinfo=`${HOME}/.nodeload`
+PROMPT_COMMAND='PS1="\[\e[1;37m\e[44m\]${project_name}\[\e[0;0m\]${prompt1}${promptinfo}${prompt2}"'
+

.projects

@@ -0,0 +1,7 @@
+#! /bin/bash
+
+function hcp_env()
+{
+source /scratch/PSB6351/envs/.env/.psb6351_environment
+}
+

psb6351_env_setup.py

@@ -0,0 +1,16 @@
+import os
+import time
+
+files = ['.bashrc', '.bash_profile', '.projects', '.env', '.nodeload']
+
+for f in files:
+    if os.path.exists(os.path.expanduser('~/%s'%f)):
+        now = ''.join(time.ctime().split(' ')).replace(':','')
+        newname = '~/%s_%s'%(f,now)
+        cmd = 'mv ~/%s %s'%(f,newname)
+        print cmd
+        os.system(cmd)
+    cmd = 'ln -s %s ~/'%os.path.abspath(f)
+    print cmd
+    os.system(cmd)
+