Spm8 batch/localization automate

spm8Batch/INSTALL_README.txt

@@ -1,6 +1,6 @@
 # # # # # # # # # # # # # # # # # #
 #
-# This is the spm8Batch processing system written by Robert C. Welsh, Ann Arbor MI
+# This is a modified version of the spm8Batch processing system written by Robert C. Welsh, Ann Arbor MI
 #
 # Copyright 2002-2012
 #
@@ -29,29 +29,21 @@
 #
 # INSTALLATION INSTRUCTIONS:
 #
-# Move the spm8Batch tar distribution file to the directory where you wish the code to 
-# reside. Then untar using
-# 
-# tar -xvf [tarfile]
 #
-# Next you will need to adjust your PATH environmental variable to include 
+# You will need to adjust your PATH environmental variable to include
 # the spm8Batch distribution
 #
-# For bash you can add this to your .bashrc or .bash_profile
-#
-#     export PATH=[spm8Batch_distribution_location]:${PATH}
-#
-# On tcsh you can add this to your .cshrc file.
+# You can do this on the fly by running "source spm8Setup" while in this directory.
+# You can also edit your .bashrc, .bash_profile, or /etc/bashrc startup scripts to source this automatically
+# for all or just some users.
 #
-#     setenv PATH [spm8Batch_distribution_location]:${PATH}
 # 
-# Next you need to implement the localization changes in spm8Batch_Global that are
-# described below. Remember the native language of the spm8Batch system is bash. An
+# Remember the native language of the spm8Batch system is bash. An
 # excellent site for BASH help is:
 # 
 #     http://tldp.org/LDP/abs/html/
 #
-# You will need to have spm8 distribution
+# You will need to have spm8 distribution (Included in this distribution)
 # 
 # You will need to have fsl, at least 4.1.7, it's known to work with 4.1.7 and 4.1.8
 #
@@ -73,7 +65,7 @@
 # -----------------------------------------------------------------
 # -----------------------------------------------------------------
 #
-# LOCALIZATION
+# LOCALIZATION (No longer needs to be edited. This section retained for developer documentation)
 #
 # The only file that has to be modified for local distrubution is the scripts "spm8Batch_Global"
 # 

spm8Batch/spm8Batch_Global

@@ -38,15 +38,18 @@ then
 # SOME GLOBAL THINGS TO CHANGE ACCORDING TO SITE
 #    
 
-    topDIR=/Users/rcwelsh/Software
+
+    curdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+    topDIR="$( cd $curdir/.. && pwd )"
 
 # You must point to SPM8 !!!
 
-    SPM8B1=${topDIR}/SPM8/spm8_with_R4667
+    SPM8B1=${topDIR}/SPM/SPM8/spm8_with_R4667
+
 
 # This is Robert Welsh's UNIX batch interface to spm8
 
-    SPM8B2=${topDIR}/spm8Batch/spm8Batch_VBM8
+    SPM8B2=${topDIR}/spm8Batch
 
 # This must point to the place where the SPM8 patch is locally. 
 
@@ -78,7 +81,7 @@ then
 # Mail job will be sent to your user name at the institutionname
 # Please set the instituion email server name here.
 
-    MAILRECPT=med.umich.edu
+    MAILRECPT=umich.edu
 
 #
 # Default email address to send messages to, on the linux machines
@@ -100,7 +103,7 @@ then
 
 # And finally, you need to point to matlab
 
-    MATLAB=/Applications/MATLAB_R2011b.app/bin/matlab
+    MATLAB=`which matlab`
 
 #    
 # Only allow author to execute code during switch.

spm8Batch/spm8Setup

@@ -1,2 +1,3 @@
+curdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
-export PATH=/net/dysthymia/spm8Batch:${PATH}
+export PATH=${curdir}:${PATH}