From bb9640cccfe77fe13ba265b4135e0345fe8400c9 Mon Sep 17 00:00:00 2001
From: Aaron Mattfeld <amattfeld@gmail.com>
Date: Tue, 31 Jan 2017 16:48:01 -0500
Subject: [PATCH] First commit adding environment setup and hw directories

---
 .bash_profile        | 25 +++++++++++++++++++++++++
 .bashrc              | 31 +++++++++++++++++++++++++++++++
 .projects            |  7 +++++++
 psb6351_env_setup.py | 16 ++++++++++++++++
 4 files changed, 79 insertions(+)
 create mode 100644 .bash_profile
 create mode 100644 .bashrc
 create mode 100644 .projects
 create mode 100644 psb6351_env_setup.py

diff --git a/.bash_profile b/.bash_profile
new file mode 100644
index 0000000..ee41f9e
--- /dev/null
+++ b/.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
diff --git a/.bashrc b/.bashrc
new file mode 100644
index 0000000..e4aaeea
--- /dev/null
+++ b/.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}"'
+
diff --git a/.projects b/.projects
new file mode 100644
index 0000000..f22119d
--- /dev/null
+++ b/.projects
@@ -0,0 +1,7 @@
+#! /bin/bash
+
+function hcp_env()
+{
+source /scratch/PSB6351/envs/.env/.psb6351_environment
+}
+
diff --git a/psb6351_env_setup.py b/psb6351_env_setup.py
new file mode 100644
index 0000000..864de32
--- /dev/null
+++ b/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)
+