updated voice env

.bashrc

@@ -1,5 +1,23 @@
+# .bashrc
+
+# Source global definitions
+if [ -f /etc/bashrc ]; then
+	. /etc/bashrc
+fi
+
+# User specific aliases and functions
+module load gcc
+module load slurm 
+
+#module add openmpi/gcc/64/1.6.5 
+#module add openblas/sandybridge/0.2.6 
+#module add lapack/gcc/64/3.4.2
+#module add fftw3/openmpi/gcc/64/3.3.3 
+#module add intel-cluster-checker/2.1.1 
+#module add intel-cluster-runtime/intel64/3.6
+
 # Export PATHs
-export PATH=/software/common/bin:$PATH
+export PATH=$HOME/bin:$PATH
 
 # Setup a fancy shell command prompt:
 prompt1="\[\e[0;33m\][\A]\[\e[0m\]" # Display the time in the bash prompt
@@ -14,14 +32,6 @@ fi
 # Aliases
 alias ls="ls --color=auto"
 
-# Setup the torque parallelization queue:
-if [ $BASH ] && [[ $TERM == xterm* ]]
-then
-    source /etc/profile.d/modules.sh
-    export LIBGL_ALWAYS_INDIRECT=yes
-    module add torque
-fi
-
 # Project specific environments
 source ~/.projects
 source ~/.custom_env

.env/.omdev_environment

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# Source Nipype, FSL, Freesurfer
+#source /software/python/setup-nipype-0.7.sh
+module add openmind/fsl/5.0.7
+module add openmind/freesurfer/5.3.0
+module add openmind/git
+
+# add PATHs
+#export ANTSPATH=/software/ANTS/versions/140107
+#export DTIPrepPATH=/software/DTIPrep/130630
+#export PATH=$DTIPrepPATH:$ANTSPATH:$PATH
+#export PATH=/software/afni:$PATH
+
+module add openmind/miniconda/3.3.0
+export CONDA_ENVS_PATH=/om/user/satra/envs
+source activate testenv
+
+# Freesurfer
+# export SUBJECTS_DIR=/mindhive/xnat/surfaces/sad
+
+# Multithreading
+export MKL_NUM_THREADS=4
+export OMP_NUM_THREADS=4
+
+# Mindboggle
+MINDBOGGLE_TOOLS=/om/user/satra/software_builds/mindboggle/mindboggle_tools/bin
+export MINDBOGGLE_TOOLS
+export PATH=$PATH:$MINDBOGGLE_TOOLS
+
+# Project name for prompt
+export project_name="SDEV"
+module add mit/matlab/2013a
+
+module add openmind/afni/2014.08.28
+module add openmind/c3d/1.0.0
+module add openmind/ants/2.1.0-1.c0c854
+
+

.env/.voice_environment

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+
+module add mit/matlab/2015a
+module add openmind/ants/2.1.0-1.c0c854
+module add openmind/freesurfer/5.3.0 
+module add openmind/fsl/5.0.7
+module add openmind/git/1.9.3
+module add openmind/c3d/1.0.0
+
+module add openmind/mricron/13.06.06
+
+
+#module add openmind/miniconda/3.7.0
+#export CONDA_ENVS_PATH=/om/project/voice/env/
+#source activate voice_env 
+module add openmind/miniconda/3.7.0
+export CONDA_ENVS_PATH=/om/user/gr21783/envs_python/
+source activate voice7
+
+# Multithreading
+export MKL_NUM_THREADS=4
+export OMP_NUM_THREADS=4
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+
+# Project name for prompt
+export project_name="voice7"
+#subjdir=/om/project/voice/mri/surfaces/
+subjdir=/om/project/voice/processedData/fsdata/
+export SUBJECTS_DIR=$subjdir
+
+#https://github.mit.edu/MGHPCC/OpenMind/wiki/Cookbook:-Getting-started#matlab
+module add openmind/srun.x11/v1
+### This opens up an interactive node:  srun.x11 -n1 -p om_interactive
+
+module add hdf5_18/1.8.12

.projects

@@ -115,6 +115,17 @@ source ~/.env/.rtsz_environment
 
 }
 
+function omdev_env()
+{
+
+source ~/.env/.omdev_environment
+}
+
+function voice_env()
+{
+source ~/.env/.voice_environment
+}
+
 function read_env()
 {
 
@@ -135,7 +146,7 @@ function simba_env()
 source ~/.env/.simba_environment
 
 }	
-<<<<<<< HEAD
+
 
 function cccbauer_env()
 {