Commits

Sean Davis committed 0d93e45

Initial commit of master module directory

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Files changed (267)

GAMESS/01May12-R2

+#%Module 1.0
+module-whatis "Sets up GAMESS 01May12-R2"
+prepend-path PATH /usr/local/apps/GAMESS/01May12-R2
+#%Module 1.0
+#
+
+set ModulesVersion 2.3-0
+#%Module 1.0
+#
+
+module-whatis "Sets up Genome Analysis Toolkit (GATK)"
+
+set 	 GATK_HOME	/usr/local/GenomeAnalysisTK-1.5-11-g5c5d8e7/
+prepend-path  PATH      $GATK_HOME
+
+# some GATK programs use Rscript in the background, so add R to the path as well
+prepend-path  PATH   	 /usr/local/R-2.15-64_cluster/bin
+
+set-alias GATK "java -Xmx1000m -jar $GATK_HOME/GenomeAnalysisTK.jar"	
+#%Module 1.0
+#
+
+module-whatis "Sets up Genome Analysis Toolkit (GATK) v 1.6-13-g91f02df"
+
+set 	 GATK_HOME	 /usr/local/gatk/GenomeAnalysisTK-1.6-13-g91f02df
+prepend-path  PATH      $GATK_HOME
+
+# some GATK programs use Rscript in the background, so add R to the path as well
+prepend-path  PATH   	 /usr/local/R-2.15-64_cluster/bin
+
+set-alias GATK "java -Xmx1000m -jar $GATK_HOME/GenomeAnalysisTK.jar"	
+#%Module 1.0
+#
+
+module-whatis "Sets up Genome Analysis Toolkit (GATK) v 2.0-36-gf5c1c1a"
+
+set 	 GATK_HOME	/usr/local/gatk/GenomeAnalysisTK-2.0-36-gf5c1c1a
+prepend-path  PATH      $GATK_HOME
+
+# some GATK programs use Rscript in the background, so add R to the path as well
+prepend-path  PATH   	 /usr/local/R-2.15-64_cluster/bin
+
+set-alias GATK "java -Xmx1000m -jar $GATK_HOME/GenomeAnalysisTK.jar"	
+#%Module 1.0
+#
+
+module-whatis "Sets up Genome Analysis Toolkit (GATK) v 2.1-11-g13c0244"
+
+set 	 GATK_HOME	/usr/local/gatk/GenomeAnalysisTK-2.1-11-g13c0244/
+prepend-path  PATH      $GATK_HOME
+
+# some GATK programs use Rscript in the background, so add R to the path as well
+prepend-path  PATH   	 /usr/local/R-2.15-64_cluster/bin
+
+set-alias GATK "java -Xmx1000m -jar $GATK_HOME/GenomeAnalysisTK.jar"	
+#%Module 1.0
+#
+ 
+module-whatis "Sets up Genome Analysis Toolkit (GATK) v 2.2-16-g9f648cb"
+
+set 	 GATK_HOME	/usr/local/gatk/GenomeAnalysisTK-2.2-16-g9f648cb/
+prepend-path  PATH      $GATK_HOME
+
+# some GATK programs use Rscript in the background, so add R to the path as well
+prepend-path  PATH   	 /usr/local/R-2.15-64_cluster/bin
+
+set-alias GATK "java -Xmx1000m -jar $GATK_HOME/GenomeAnalysisTK.jar"	
+#%Module 1.0
+#
+
+module-whatis "Sets up Genome Analysis Toolkit (GATK) v 2.2-8-gec077cd"
+
+set 	 GATK_HOME	/usr/local/gatk/GenomeAnalysisTK-2.2-8-gec077cd/
+prepend-path  PATH      $GATK_HOME
+
+# some GATK programs use Rscript in the background, so add R to the path as well
+prepend-path  PATH   	 /usr/local/R-2.15-64_cluster/bin
+
+set-alias GATK "java -Xmx1000m -jar $GATK_HOME/GenomeAnalysisTK.jar"	
+#%Module 1.0
+#
+ 
+module-whatis "Sets up Genome Analysis Toolkit (GATK) v GenomeAnalysisTK-2.3-0-g9593e74"
+
+set 	 GATK_HOME	/usr/local/gatk/GenomeAnalysisTK-2.3-0-g9593e74
+prepend-path  PATH      $GATK_HOME
+
+# some GATK programs use Rscript in the background, so add R to the path as well
+prepend-path  PATH   	 /usr/local/R-2.15-64_cluster/bin
+
+set-alias GATK "java -Xmx1000m -jar $GATK_HOME/GenomeAnalysisTK.jar"	
+#%Module 1.0
+#
+
+module-whatis "Sets up MMTSB"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/mmtsb_toolset/perl
+prepend-path  PATH          /usr/local/mmtsb_toolset/bin
+setenv MMTSBDIR       /usr/local/mmtsb_toolset
+setenv REMOTESHELL    rsh 		
+#%Module 1.0
+#
+#  R module for use with 'environment-modules' package on helix:
+# 
+
+module-whatis "Sets up R 2.14 on helix/biowulf cluster"
+
+# Define LD_LIBRARY_PATH
+prepend-path LD_LIBRARY_PATH /usr/lib64
+prepend-path LD_LIBRARY_PATH /usr/local/GSL/1.15/lib
+prepend-path LD_LIBRARY_PATH /usr/local/ROOT/lib/root
+prepend-path LD_LIBRARY_PATH /usr/local/graphviz/lib64
+prepend-path LD_LIBRARY_PATH /usr/local/netcdf/4.1.2/lib
+
+# Define PATH
+prepend-path PATH /usr/local/netcdf/4.1.2/bin
+prepend-path PATH /usr/local/GSL/1.15/bin
+prepend-path PATH /usr/local/ROOT/bin
+prepend-path PATH /usr/local/graphviz/bin
+
+# Define environment variables
+setenv PERL /usr/local/perl-5.8.9/bin/perl
+setenv GSL_INC /usr/local/GSL/1.15/include/gsl
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    prepend-path LD_LIBRARY_PATH /usr/local/ATLAS/current/intel_X5550
+    setenv JAGS_INCLUDE /local/JAGS-3.2.0/include/JAGS
+    setenv JAGS_LIB /local/lib64
+    setenv JAGS_MODULES /local/lib64/JAGS/modules-3
+    # Set aliases for R
+    set-alias "R" "/usr/local/R-2.14-64/bin/R"
+    set-alias "Rscript" "/local/R-2.14-64/bin/Rscript"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # R should not run on the biowulf head node
+       puts stderr "R sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/R.html for"
+       puts stderr "information on using R on Biowulf."
+       puts stderr " "
+       break
+   } else {
+       prepend-path LD_LIBRARY_PATH /usr/local/ATLAS/current/default
+       prepend-path LD_LIBRARY_PATH /usr/local/openmpi/lib
+       prepend-path PATH /usr/local/openmpi/bin
+       setenv JAGS_INCLUDE /usr/local/JAGS-3.2.0/include/JAGS
+       setenv JAGS_LIB /usr/local/lib64
+       setenv JAGS_MODULES /usr/local/lib64/JAGS/modules-3
+       set-alias "R" "/usr/local/R-2.14-64_cluster/bin/R"
+       set-alias "Rscript" "/usr/local/R-2.14-64_cluster/bin/Rscript"       
+      }
+  }
+
+
+
+#%Module 1.0
+#
+#  R module for use with 'environment-modules' package on helix:
+# 
+
+module-whatis "Sets up R 2.14 on helix/biowulf cluster"
+
+# Define LD_LIBRARY_PATH
+prepend-path LD_LIBRARY_PATH /usr/lib64
+prepend-path LD_LIBRARY_PATH /usr/local/GSL/1.15/lib
+prepend-path LD_LIBRARY_PATH /usr/local/ROOT/lib/root
+prepend-path LD_LIBRARY_PATH /usr/local/graphviz/lib64
+prepend-path LD_LIBRARY_PATH /usr/local/netcdf/4.1.2/lib
+
+# Define PATH
+prepend-path PATH /usr/local/netcdf/4.1.2/bin
+prepend-path PATH /usr/local/GSL/1.15/bin
+prepend-path PATH /usr/local/ROOT/bin
+prepend-path PATH /usr/local/graphviz/bin
+
+# Define environment variables
+setenv PERL /usr/local/perl-5.8.9/bin/perl
+setenv GSL_INC /usr/local/GSL/1.15/include/gsl
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    prepend-path LD_LIBRARY_PATH /usr/local/ATLAS/current/intel_X5550
+    setenv JAGS_INCLUDE /local/JAGS-3.2.0/include/JAGS
+    setenv JAGS_LIB /local/lib64
+    setenv JAGS_MODULES /local/lib64/JAGS/modules-3
+    # Set aliases for R
+    set-alias "R" "/local/R-2.15.1-64/bin/R"
+    set-alias "Rscript" "/local/R-2.15.1-64/bin/Rscript"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # R should not run on the biowulf head node
+       puts stderr "R sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/R.html for"
+       puts stderr "information on using R on Biowulf."
+       puts stderr " "
+       break
+   } else {
+       prepend-path LD_LIBRARY_PATH /usr/local/ATLAS/current/default
+       prepend-path LD_LIBRARY_PATH /usr/local/openmpi/lib
+       prepend-path PATH /usr/local/openmpi/bin
+       setenv JAGS_INCLUDE /usr/local/JAGS-3.2.0/include/JAGS
+       setenv JAGS_LIB /usr/local/lib64
+       setenv JAGS_MODULES /usr/local/lib64/JAGS/modules-3
+       set-alias "R" "/usr/local/R-2.15.1-64_cluster/bin/R"
+       set-alias "Rscript" "/usr/local/R-2.15.1-64_cluster/bin/Rscript"       
+      }
+  }
+
+
+
+#%Module 1.0
+#
+
+module-whatis "Sets up ViennaRNA"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/viennarna/bin
+ 		
+#%Module 1.0
+#
+set ModulesVersion 1.3.4
+#%Module 1.0
+#
+
+module-whatis "Sets up abyss 1.3.1"
+
+prepend-path  PATH   	 /usr/local/abyss-1.3.1/bin
+prepend-path PATH /usr/local/transabyss/
+prepend-path PATH /usr/local/openmpi/bin
+#%Module 1.0
+#
+
+module-whatis "Sets up abyss 1.3.2"
+
+prepend-path  PATH   	 /usr/local/abyss-1.3.2/bin
+prepend-path PATH /usr/local/transabyss/
+prepend-path PATH /usr/local/openmpi/bin
+#%Module 1.0
+#
+
+module-whatis "Sets up abyss 1.3.4"
+
+prepend-path  PATH   	 /usr/local/abyss-1.3.4/bin
+prepend-path PATH /usr/local/transabyss/
+prepend-path PATH /usr/local/openmpi/bin
+#%Module 1.0
+#
+set 	ModulesVersion 18Oct2012
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up AFNI and SUMA"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/afni-18-oct-2012/linux_glibc22/
+prepend-path  PATH          /usr/local/ctf/ 		

afni/18Oct2012-openmp

+#%Module 1.0
+#
+
+module-whatis "Sets up AFNI and SUMA"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/afni-18-oct-2012/linux_openmp_64
+prepend-path  PATH          /usr/local/ctf 		
+#%Module 1.0
+#
+
+module-whatis "Sets up AFNI and SUMA"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/afni-21-Dec-2011/linux_gcc33_64/
+prepend-path  PATH          /usr/local/ctf
+ 		
+#%Module 1.0
+#
+#  Amber 12 module for use with 'environment-modules' package:
+# 
+
+module-whatis "Amber version 12"
+
+set ModulesVersion 12
+#%Module 1.0
+#
+#  Amber 12 module for use with 'environment-modules' package:
+# 
+
+module-whatis "Amber version 10 for Gigabit ethernet"
+
+setenv AMBERHOME /usr/local/amber10/
+# Define PATHs
+prepend-path  PATH          /usr/local/amber10/exe
+
+ 		
+#%Module 1.0
+#
+#  Amber 12 module for use with 'environment-modules' package:
+# 
+
+module-whatis "Amber version 10 for Gigabit ethernet"
+
+setenv AMBERHOME /usr/local/amber10/
+# Define PATHs
+prepend-path  PATH          /usr/local/amber10/exe.ipath
+
+
+
+ 		
+#%Module 1.0
+#
+#  Amber 12 module for use with 'environment-modules' package:
+# 
+
+module-whatis "Amber version 11"
+
+setenv AMBERHOME /usr/local/amber11
+
+# Define PATHs
+prepend-path  PATH          /usr/local/amber11/exe
+ 		
+#%Module 1.0
+#
+#  Amber 12 module for use with 'environment-modules' package:
+# 
+
+module-whatis "Amber version 11"
+
+setenv AMBERHOME /usr/local/amber11
+
+# Define PATHs
+prepend-path  PATH          /usr/local/amber11/exe
+ 		
+#%Module 1.0
+#
+#  Amber 12 module for use with 'environment-modules' package:
+# 
+
+module-whatis "Amber version 12"
+
+setenv AMBERHOME /usr/local/amber12
+# Define PATHs
+prepend-path  PATH          /usr/local/amber12/exe
+ 		

annovar/2012-02-23

+#%Module 1.0
+#
+
+module-whatis "Sets up Annovar"
+prepend-path PATH /usr/local/annovar-2012-02-23
+setenv ANNOVAR_HOME /usr/local/annovar-2012-02-23
+setenv ANNOVAR_DATA /fdb/annovar/2012-08-17

annovar/2012-05-25

+#%Module 1.0
+#
+
+module-whatis "Sets up Annovar"
+prepend-path PATH /usr/local/annovar-2012-05-25
+setenv ANNOVAR_HOME /usr/local/annovar-2012-05-25
+setenv ANNOVAR_DATA /fdb/annovar/2012-08-17

annovar/2012-10-23

+#%Module 1.0
+#
+
+module-whatis "Sets up Annovar"
+prepend-path PATH /usr/local/annovar-2012-10-23
+setenv ANNOVAR_HOME /usr/local/annovar-2012-10-23
+setenv ANNOVAR_DATA /fdb/annovar/2012-11-08
+#%Module 1.0
+
+module-whatis "Sets up APBS v1.1.0"
+
+append-path PATH /usr/local/apbs-1.1.0/bin
+#%Module 1.0
+
+module-whatis "Sets up APBS v1.2.0"
+
+append-path PATH /usr/local/apbs-1.2.0/bin
+#%Module 1.0
+
+module-whatis "Sets up APBS v1.2.1"
+
+append-path PATH /usr/local/apbs-1.2.1-amd64/bin
+#%Module 1.0
+
+module-whatis "Sets up APBS v1.3"
+
+append-path PATH /usr/local/apbs-1.3-src/bin
+#%Module 1.0
+
+module-whatis "Sets up APBS v1.4"
+
+append-path PATH /usr/local/apbs-1.4/bin
+#%Module 1.0
+#
+set ModulesVersion 1.15.0
+#%Module 1.0
+#
+
+module-whatis "Sets up apt-1.14.3-amd64-pc-linux"
+
+prepend-path  PATH   	 /usr/local/apt-1.14.3-amd64-pc-linux/bin
+prepend-path PATH /usr/local/GCC/4.7.0/bin
+
+prepend-path LD_LIBRARY_PATH /usr/local/GCC/4.7.0/lib64
+prepend-path MANPATH /usr/local/GCC/4.7.0/man
+
+setenv CC gcc
+setenv CXX g++
+setenv FC gfortran
+setenv F77 gfortran
+setenv F90 gfortran
+setenv F95 gfortran
+#%Module 1.0
+#
+
+module-whatis "Sets up apt-1.14.3.1"
+
+prepend-path  PATH   	 /usr/local/apt-1.14.3.1/bin
+prepend-path PATH /usr/local/GCC/4.7.0/bin
+
+prepend-path LD_LIBRARY_PATH /usr/local/GCC/4.7.0/lib64
+prepend-path MANPATH /usr/local/GCC/4.7.0/man
+
+setenv CC gcc
+setenv CXX g++
+setenv FC gfortran
+setenv F77 gfortran
+setenv F90 gfortran
+setenv F95 gfortran
+#%Module 1.0
+#
+
+module-whatis "Sets up apt-1.15.0"
+
+prepend-path  PATH   	 /usr/local/apt-1.15.0-x86_64-intel-linux/bin
+prepend-path PATH /usr/local/GCC/4.7.0/bin
+
+prepend-path LD_LIBRARY_PATH /usr/local/GCC/4.7.0/lib64
+prepend-path MANPATH /usr/local/GCC/4.7.0/man
+
+setenv CC gcc
+setenv CXX g++
+setenv FC gfortran
+setenv F77 gfortran
+setenv F90 gfortran
+setenv F95 gfortran
+#%Module 1.0
+#
+
+module-whatis "Sets up bam2fastq 1.1.0"
+
+prepend-path  PATH   	 /usr/local/bam2fastq

bamtools/.version

+#%Module 1.0
+#
+set ModulesVersion 2.2.0
+#%Module 1.0
+#
+
+module-whatis "Sets up bamtools 2.1.1"
+
+prepend-path  PATH   	 /usr/local/bamtools-2.1.1/bin
+prepend-path LD_LIBRARY_PATH /usr/local/bamtools-2.1.1/lib/
+#%Module 1.0
+#
+
+module-whatis "Sets up bamtools 2.2.0"
+
+prepend-path  PATH   	 /usr/local/bamtools-2.2.0/bin
+prepend-path LD_LIBRARY_PATH /usr/local/bamtools-2.2.0/lib/
+#%Module 1.0
+#
+
+module-whatis "Sets up bamutil"
+
+prepend-path  PATH   	 /usr/local/bamutil/bamUtil/bin
+

bedtools/.version

+#%Module 1.0
+#
+set ModulesVersion 2.17.0
+
+#%Module 1.0
+#
+
+module-whatis "Sets up bedtools 2.17.0"
+
+prepend-path  PATH   	 /usr/local/bedtools-2.17.0/bin/
+#%Module 1.0
+#
+
+module-whatis "Sets up bedtools 2.5.1"
+
+prepend-path  PATH   	 /usr/local/bedtools_2.5.1/bin
+#%Module 1.0
+#
+
+module-whatis "Sets up bedtools 2.7.1"
+
+prepend-path  PATH   	 /usr/local/bedtools_2.7.1/bin/
+#%Module 1.0
+#
+
+module-whatis "Sets up bfast"
+prepend-path  PATH   	 /usr/local/bfast/bin
+#%Module 1.0
+#
+
+module-whatis "Sets up bfast+bwa"
+prepend-path  PATH   	 /usr/local/bfast+bwa/bin
+#%Module 1.0
+#
+
+module-whatis "Sets up NCBI Blast 2.2.26"
+
+prepend-path  PATH          /usr/local/blast/blast-2.2.26/bin
+prepend-path  PATH          /usr/local/blast/bin
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up NCBI Blast 2.2.27+"
+
+prepend-path  PATH          /usr/local/blast/blast-2.2.27+/bin
+ 		
+#%Module 1.0
+#
+set ModulesVersion 2-2.0.2
+#%Module 1.0
+#
+
+module-whatis "Sets up bowtie"
+
+prepend-path  PATH   	 /usr/local/bowtie-0.12.8
+

bowtie/2-2.0.0-beta7

+#%Module 1.0
+#
+
+module-whatis "Sets up bowtie"
+
+prepend-path  PATH   	 /usr/local/bowtie2-2.0.0-beta7
+
+#%Module 1.0
+#
+
+module-whatis "Sets up bowtie"
+
+prepend-path  PATH   	 /usr/local/bowtie2-2.0.2
+#%Module 1.0
+#
+
+module-whatis "Sets up BSoft 1.8"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/bsoft-1.8/bin
+
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up BSoft 1.8.2"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/bsoft-1.8.2/bin
+
+
+ 		
+#%Module 1.0
+#
+set ModulesVersion 0.6.2
+#%Module 1.0
+#
+
+module-whatis "Sets up bwa 0.5.9"
+
+prepend-path  PATH   	 /usr/local/bwa-0.5.9
+#%Module 1.0
+#
+
+module-whatis "Sets up bwa 0.6.2"
+
+prepend-path  PATH   	 /usr/local/bwa-0.6.2
+#%Module 1.0
+#
+set ModulesVersion 1.8.2
+
+#%Module 1.0
+#
+
+module-whatis "Sets up casava 1.8.0"
+
+prepend-path  PATH   	 /usr/local/CASAVA_v1.8.0/bin
+
+#%Module 1.0
+#
+
+module-whatis "Sets up casava 1.8.2"
+
+prepend-path  PATH   	 /usr/local/CASAVA_v1.8.2/bin
+

chromopainter/0.0.1

+#%Module 1.0
+#
+
+module-whatis "Sets up ChromoPainter"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/chromopainter/bin
+prepend-path  LD_LIBRARY_PATH          /usr/local/gsl/64/lib
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up CMAKE 2.8.0"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/cmake-2.8.0/bin
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up CUDA 2.3"
+
+setenv		CUDA_HOME	/usr/local/cuda2.3
+prepend-path	PATH		/usr/local/cuda2.3/bin
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up CUDA 3.0"
+
+setenv 		CUDA_HOME  	/usr/local/cuda3.0
+prepend-path  	PATH      	/usr/local/cuda3.0/bin
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up CUDA 3.1"
+
+setenv CUDA_HOME    /usr/local/cuda3.1
+prepend-path  PATH          /usr/local/cuda3.1/bin
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up CUDA 4.0.17"
+
+setenv CUDA_HOME  /usr/local/cuda4.0.17
+prepend-path  PATH          /usr/local/cuda4.0.17/bin
+
+ 		
+#%Module1.0#####################################################################
+##
+## dot modulefile
+##
+## modulefiles/dot.  Generated from dot.in by configure.
+##
+proc ModulesHelp { } {
+	global dotversion
+
+	puts stderr "\tAdds `.' to your PATH environment variable"
+	puts stderr "\n\tThis makes it easy to add the current working directory"
+	puts stderr "\tto your PATH environment variable.  This allows you to"
+	puts stderr "\trun executables in your current working directory"
+	puts stderr "\twithout prepending ./ to the excutable name"
+	puts stderr "\n\tVersion $dotversion\n"
+}
+
+module-whatis	"adds `.' to your PATH environment variable"
+
+# for Tcl script use only
+set	dotversion	3.2.9
+
+append-path	PATH	.
+
+#%Module 1.0
+#
+#  Matlab  module for use with 'environment-modules' package on helix:
+# 
+
+module-whatis "Sets up dvipng on helix/biowulf cluster"
+
+prepend-path LD_LIBRARY_PATH /usr/local/lib
+
+
+
+#%Module 1.0
+
+module-whatis "Sets up EMAN2 v2.04"
+
+setenv EMAN2DIR /usr/local/EMAN2-2.04
+prepend-path PATH /usr/local/openmpi_gnu_eth/bin
+prepend-path PATH /usr/local/EMAN2-2.04/bin
+prepend-path PATH /usr/local/EMAN2-2.04/Python/bin
+prepend-path LD_LIBRARY_PATH /usr/local/EMAN2-2.04/lib
+prepend-path PYTHONPATH /usr/local/EMAN2-2.04/bin
+prepend-path PYTHONPATH /usr/local/EMAN2-2.04/lib
+#%Module 1.0
+
+module-whatis "Sets up EMAN2 v2.05"
+
+setenv EMAN2DIR /usr/local/EMAN2-2.05_120514
+prepend-path PATH /usr/local/openmpi-1.2.9_gnu_eth_PBS/bin
+prepend-path PATH /usr/local/EMAN2-2.05_120514/bin
+prepend-path PATH /usr/local/EMAN2-2.05_120514/Python/bin
+prepend-path LD_LIBRARY_PATH /usr/local/openmpi-1.2.9_gnu_eth_PBS/lib
+prepend-path LD_LIBRARY_PATH /usr/local/EMAN2-2.05_120514/lib
+prepend-path PYTHONPATH /usr/local/EMAN2-2.05_120514/bin
+prepend-path PYTHONPATH /usr/local/EMAN2-2.05_120514/lib
+#%Module 1.0
+
+module-whatis "Sets up EMAN2 v2.06"
+
+setenv EMAN2DIR /usr/local/EMAN2-2.06
+prepend-path PATH /usr/local/OpenMPI/openmpi-1.2.9_gnu_eth_PBS/bin
+prepend-path PATH /usr/local/EMAN2-2.06/bin
+prepend-path PATH /usr/local/EMAN2-2.06/Python/bin
+prepend-path LD_LIBRARY_PATH /usr/local/OpenMPI/openmpi-1.2.9_gnu_eth_PBS/lib
+prepend-path LD_LIBRARY_PATH /usr/local/EMAN2-2.06/lib
+prepend-path PYTHONPATH /usr/local/EMAN2-2.06/bin
+prepend-path PYTHONPATH /usr/local/EMAN2-2.06/lib

eman2/2.06_121120

+#%Module 1.0
+
+module-whatis "Sets up EMAN2 v2.06_121120"
+
+setenv EMAN2DIR /usr/local/EMAN2-2.06_121120
+prepend-path PATH /usr/local/OpenMPI/openmpi-1.2.9_gnu_eth_PBS/bin
+prepend-path PATH /usr/local/EMAN2-2.06_121120/bin
+prepend-path PATH /usr/local/EMAN2-2.06_121120/Python/bin
+prepend-path LD_LIBRARY_PATH /usr/local/OpenMPI/openmpi-1.2.9_gnu_eth_PBS/lib
+prepend-path LD_LIBRARY_PATH /usr/local/EMAN2-2.06_121120/lib
+prepend-path PYTHONPATH /usr/local/EMAN2-2.06_121120/bin
+prepend-path PYTHONPATH /usr/local/EMAN2-2.06_121120/lib
+#prepend-path LD_LIBRARY_PATH /usr/local/GCC/gcc-4.5.1/lib
+#prepend-path LD_LIBRARY_PATH /usr/local/GCC/gcc-4.5.1/lib64
+#%Module 1.0
+
+module-whatis "Sets up EMAN2 v2.06"
+
+setenv EMAN2DIR /home/hooverdm/EMAN2
+#prepend-path PATH /usr/local/OpenMPI/openmpi-1.2.9_gnu_ib_PBS/bin
+#prepend-path LD_LIBRARY_PATH /usr/local/OpenMPI/openmpi-1.2.9_gnu_ib_PBS/lib
+prepend-path PATH /usr/local/OpenMPI/openmpi-1.4.3_intel_ib/bin
+prepend-path LD_LIBRARY_PATH /usr/local/OpenMPI/openmpi-1.4.3_intel_ib/lib
+prepend-path PATH /home/hooverdm/EMAN2/bin
+prepend-path PATH /home/hooverdm/EMAN2/Python/bin
+prepend-path LD_LIBRARY_PATH /home/hooverdm/EMAN2/lib
+prepend-path PYTHONPATH /home/hooverdm/EMAN2/bin
+prepend-path PYTHONPATH /home/hooverdm/EMAN2/lib
+#%Module 1.0
+#
+
+module-whatis "Sets up express 1.2.2"
+
+prepend-path  PATH   	 /usr/local/express-1.2.2-src
+#%Module 1.0
+#
+
+setenv CFLAGS	-I/usr/local/fftw3/include
+setenv LDFLAGS  -L/usr/local/fftw3/lib
+#%Module 1.0
+#
+set ModulesVersion 5.0
+#%Module 1.0
+#
+
+module-whatis "Sets up FSL 5.0"
+
+setenv FSLDIR /usr/local/fsl-4.1.8
+setenv POSSUMDIR /usr/local/fsl-4.1.8
+prepend-path  PATH          /usr/local/fsl-4.1.8/bin
+
+# environment variables from $FSLDIR/etc/fslconf/fsl.csh
+setenv FSLOUTPUTTYPE NIFTI_GZ
+setenv FSLMULTIFILEQUIT TRUE
+setenv FSLTCLSH /usr/local/fsl-4.1.8/bin/fsltclsh
+setenv FSLWISH /usr/local/fsl-4.1.8/bin/fslwish
+setenv FSLLOCKDIR 1
+setenv FSLMACHINELIST 1
+setenv FSLREMOTECALL 1
+setenv FSLCONFDIR /usr/local/fsl-4.1.8/config
+setenv FSLMACHTYPE `/usr/local/fsl-4.1.8/etc/fslconf/fslmachtype.sh`
+
+#%Module 1.0
+#
+
+module-whatis "Sets up FSL 5.0"
+
+setenv FSLDIR /usr/local/fsl-4.1.9
+setenv POSSUMDIR /usr/local/fsl-4.1.9
+prepend-path  PATH          /usr/local/fsl-4.1.9/bin
+
+# environment variables from $FSLDIR/etc/fslconf/fsl.csh
+setenv FSLOUTPUTTYPE NIFTI_GZ
+setenv FSLMULTIFILEQUIT TRUE
+setenv FSLTCLSH /usr/local/fsl-4.1.9/bin/fsltclsh
+setenv FSLWISH /usr/local/fsl-4.1.9/bin/fslwish
+setenv FSLLOCKDIR 1
+setenv FSLMACHINELIST 1
+setenv FSLREMOTECALL 1
+setenv FSLCONFDIR /usr/local/fsl-4.1.9/config
+setenv FSLMACHTYPE `/usr/local/fsl-4.1.9/etc/fslconf/fslmachtype.sh`
+
+#%Module 1.0
+#
+
+module-whatis "Sets up FSL 5.0"
+
+setenv FSLDIR /usr/local/fsl-5.0/fsl
+setenv POSSUMDIR /usr/local/fsl-5.0/fsl
+prepend-path  PATH          /usr/local/fsl-5.0/fsl/bin
+
+# environment variables from $FSLDIR/etc/fslconf/fsl.csh
+setenv FSLOUTPUTTYPE NIFTI_GZ
+setenv FSLMULTIFILEQUIT TRUE
+setenv FSLTCLSH /usr/local/fsl-5.0/fsl/bin/fsltclsh
+setenv FSLWISH /usr/local/fsl-5.0/fsl/bin/fslwish
+setenv FSLLOCKDIR 1
+setenv FSLMACHINELIST 1
+setenv FSLREMOTECALL 1
+setenv FSLCONFDIR /usr/local/fsl-5.0/fsl/config
+setenv FSLMACHTYPE `/usr/local/fsl-5.0/fsl/etc/fslconf/fslmachtype.sh`
+

fusionmap/.version

+#%Module 1.0
+#
+set ModulesVersion 2012-12-08

fusionmap/2012-01-01

+#%Module 1.0
+#
+
+module-whatis "Sets up FusionMap 2012-01-01"
+
+prepend-path  PATH          /usr/local/mono-2.8.1/bin
+prepend-path  PATH          /usr/local/FusionMap_2012-12-08/bin
+
+	
+ 		

fusionmap/2012-12-08

+#%Module 1.0
+#
+
+module-whatis "Sets up FusionMap 2012-12-08"
+
+prepend-path  PATH          /usr/local/mono-2.10.8/bin
+prepend-path  PATH          /usr/local/FusionMap_2012-12-08/bin
+
+	
+ 		
+#%Module 1.0
+#
+set ModulesVersion 10
+#%Module 1.0
+#
+
+module-whatis "Sets up Gauss 10"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/gauss-10
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up Gauss 3.2"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/gauss-3.2
+
+ 		

gaussian/.version

+#%Module 1.0
+#
+set     ModulesVersion g09-B01
+#%Module 1.0
+#
+
+module-whatis "Sets up Gaussian 09 v A.02"
+
+# check if the user is in the gaussian group
+set return [system /usr/bin/groups | /bin/grep -q gaussian]
+if { $return != 0 } {
+  puts stderr "All users of Gaussian09 need to belong to the gaussian group."
+  puts stderr "Please contact the Helix staff (staff@helix.nih.gov) for more information."
+  puts stderr ""
+  break
+}
+
+# don't allow jobs on biowulf head node
+set hostname [exec /bin/uname -n]
+if { $hostname == "biowulf.nih.gov" }  {
+  puts stderr "NO RUNNING ON biowulf.nih.gov!  Please use an interactive node or submit this through the batch system."
+  break
+}
+
+prepend-path LD_LIBRARY_PATH /usr/local/gaussian09-A02-64/g09/bsd:/usr/local/gaussian09-A02-64/g09/local:/usr/local/gaussian09-A02-64/g09/extras:/usr/local/gaussian09-A02-64/g09
+
+# gv lib has to be at the end
+append-path LD_LIBRARY_PATH /usr/local/gaussian09-A02-64/gv/lib
+
+setenv g09root /usr/local/gaussian09-A02-64
+setenv _DSM_BARRIER SHM
+setenv G09BASIS /usr/local/gaussian09-A02-64/g09/basis
+setenv GAUSS_ARCHDIR /usr/local/gaussian09-A02-64/g09/arch
+setenv GAUSS_BSDDIR /usr/local/gaussian09-A02-64/g09/bsd
+setenv GAUSS_EXEDIR /usr/local/gaussian09-A02-64/g09/bsd:/usr/local/gaussian09-A02-64/g09/local:/usr/local/gaussian09-A02-64/g09/extras:/usr/local/gaussian09-A02-64/g09
+setenv GAUSS_LEXEDIR /usr/local/gaussian09-A02-64/g09/linda-exe
+setenv GV_DIR /usr/local/gaussian09-A02-64/gv
+setenv LINDA_FORTRAN_LINK "pgf77 -Bstatic_pgi -mp=nonuma -tp k8-64 -i8 -r8 -mcmodel=medium"
+setenv LINDA_FORTRAN "pgf77 -Bstatic_pgi -mp=nonuma -tp k8-64 -i8 -r8 -mcmodel=medium"
+setenv MAKEFLAGS "CSIZE=1048576 CSIZEW=128 OPTOI= MMODEL='-mcmodel=medium' I8FLAG=-i8 R8FLAG=-r8 I8CPP1=-DI64 I8CPP2=-DP64 I8CPP3=-DPACK64 I8CPP4=-DUSE_I2 MACHTY=k8-64 GAULIBU=util.a BLAS1=bsd/libf77blas-amd64.a BLAS2=bsd/libatlas-amd64.a"
+
+append-path PATH /usr/local/gaussian09-A02-64/g09/bsd:/usr/local/gaussian09-A02-64/g09/local:/usr/local/gaussian09-A02-64/g09/extras:/usr/local/gaussian09-A02-64/g09
+
+append-path PERLLIB /usr/local/gaussian09-A02-64/g09/bsd
+append-path PERL5LIB /usr/local/gaussian09-A02-64/g09/bsd
+
+setenv PGIDIR /usr/pgi/unknown
+setenv PGI_TERM trace,abort
+setenv PGI /usr/pgi
+setenv POSTFL_FORTRAN "pgf77 -Bstatic_pgi -mp=nonuma -tp k8-64 -i8 -r8 -mcmodel=medium"
+setenv _RLD_ARGS "-log /dev/null"
+
+# set GAUSS_SCRDIR if not assigned and directory exists
+if {![info exists ::env(GAUSS_SCRDIR)]} {
+  setenv GAUSS_SCRDIR /scratch
+} else {
+  if {![file exists $::env(GAUSS_SCRDIR)]} {
+    puts stderr "GAUSS_SCRDIR ($env(GAUSS_SCRDIR)) does not exist"
+    puts stderr "GAUSS_SCRDIR set to /scratch"
+    setenv GAUSS_SCRDIR /scratch
+  } else {
+    if {![file isdirectory $::env(GAUSS_SCRDIR)]} {
+      puts stderr "GAUSS_SCRDIR ($env(GAUSS_SCRDIR)) is not a directory"
+      puts stderr "GAUSS_SCRDIR set to /scratch"
+      setenv GAUSS_SCRDIR /scratch
+    }
+  }
+}
+
+# set GAUSS_LFLAGS if on a node
+if {[info exists ::env(PBS_NODEFILE)]} {
+  set nodelist [exec /usr/bin/tr "\n" " " < $::env(PBS_NODEFILE) ]
+  setenv GAUSS_LFLAGS "-nodelist $nodelist"
+}
+
+set-alias g09 /usr/local/gaussian09-A02-64/g09/g09
+set-alias gaussview /usr/local/gaussian09-A02-64/gv/gview
+#%Module 1.0
+#
+
+module-whatis "Sets up Gaussian 09 v B.01"
+
+# check if the user is in the gaussian group
+set return [system /usr/bin/groups | /bin/grep -q gaussian]
+if { $return != 0 } {
+  puts stderr "All users of Gaussian09 need to belong to the gaussian group."
+  puts stderr "Please contact the Helix staff (staff@helix.nih.gov) for more information."
+  puts stderr ""
+  break
+}
+
+# don't allow jobs on biowulf head node
+set hostname [exec /bin/uname -n]
+if { $hostname == "biowulf.nih.gov" }  {
+  puts stderr "NO RUNNING ON biowulf.nih.gov!  Please use an interactive node or submit this through the batch system."
+  break
+}
+
+prepend-path LD_LIBRARY_PATH /usr/local/gaussian09-B01-64/g09/bsd:/usr/local/gaussian09-B01-64/g09/local:/usr/local/gaussian09-B01-64/g09/extras:/usr/local/gaussian09-B01-64/g09
+
+# gv lib has to be at the end
+append-path LD_LIBRARY_PATH /usr/local/gaussian09-B01-64/gv/lib
+
+setenv g09root /usr/local/gaussian09-B01-64
+setenv _DSM_BARRIER SHM
+setenv G09BASIS /usr/local/gaussian09-B01-64/g09/basis
+setenv GAUSS_ARCHDIR /usr/local/gaussian09-B01-64/g09/arch
+setenv GAUSS_BSDDIR /usr/local/gaussian09-B01-64/g09/bsd
+setenv GAUSS_EXEDIR /usr/local/gaussian09-B01-64/g09/bsd:/usr/local/gaussian09-B01-64/g09/local:/usr/local/gaussian09-B01-64/g09/extras:/usr/local/gaussian09-B01-64/g09
+setenv GAUSS_LEXEDIR /usr/local/gaussian09-B01-64/g09/linda-exe
+setenv GV_DIR /usr/local/gaussian09-B01-64/gv
+setenv LINDA_FORTRAN_LINK "pgf77 -Bstatic_pgi -mp=nonuma -tp k8-64 -i8 -r8 -mcmodel=medium"
+setenv LINDA_FORTRAN "pgf77 -Bstatic_pgi -mp=nonuma -tp k8-64 -i8 -r8 -mcmodel=medium"
+setenv MAKEFLAGS "CSIZE=1048576 CSIZEW=128 OPTOI= MMODEL='-mcmodel=medium' I8FLAG=-i8 R8FLAG=-r8 I8CPP1=-DI64 I8CPP2=-DP64 I8CPP3=-DPACK64 I8CPP4=-DUSE_I2 MACHTY=k8-64 GAULIBU=util.a BLAS1=bsd/libf77blas-amd64.a BLAS2=bsd/libatlas-amd64.a"
+
+prepend-path PATH /usr/local/gaussian09-B01-64/g09/bsd:/usr/local/gaussian09-B01-64/g09/local:/usr/local/gaussian09-B01-64/g09/extras:/usr/local/gaussian09-B01-64/g09
+
+append-path PERLLIB /usr/local/gaussian09-B01-64/g09/bsd
+append-path PERL5LIB /usr/local/gaussian09-B01-64/g09/bsd
+
+setenv PGIDIR /usr/pgi/unknown
+setenv PGI_TERM trace,abort
+setenv PGI /usr/pgi
+setenv POSTFL_FORTRAN "pgf77 -Bstatic_pgi -mp=nonuma -tp k8-64 -i8 -r8 -mcmodel=medium"
+setenv _RLD_ARGS "-log /dev/null"
+
+# set GAUSS_SCRDIR if not assigned and directory exists
+if {![info exists ::env(GAUSS_SCRDIR)]} {
+  setenv GAUSS_SCRDIR /scratch
+} else {
+  if {![file exists $::env(GAUSS_SCRDIR)]} {
+    puts stderr "GAUSS_SCRDIR ($env(GAUSS_SCRDIR)) does not exist"
+    puts stderr "GAUSS_SCRDIR set to /scratch"
+    setenv GAUSS_SCRDIR /scratch
+  } else {
+    if {![file isdirectory $::env(GAUSS_SCRDIR)]} {
+      puts stderr "GAUSS_SCRDIR ($env(GAUSS_SCRDIR)) is not a directory"
+      puts stderr "GAUSS_SCRDIR set to /scratch"
+      setenv GAUSS_SCRDIR /scratch
+    }
+  }
+}
+
+# set GAUSS_LFLAGS if on a node
+if {[info exists ::env(PBS_NODEFILE)]} {
+  set nodelist [exec /usr/bin/tr "\n" " " < $::env(PBS_NODEFILE) ]
+  setenv GAUSS_LFLAGS "-nodelist $nodelist"
+}
+
+set-alias g09 /usr/local/gaussian09-B01-64/g09/g09
+set-alias gaussview /usr/local/gaussian09-B01-64/gv/gview
+#%Module 1.0
+module-whatis "Sets up gcc 4.5.1"
+
+prepend-path PATH /usr/local/GCC/gcc-4.5.1/bin
+prepend-path LD_LIBRARY_PATH /usr/local/GCC/gcc-4.5.1/lib
+prepend-path LD_LIBRARY_PATH /usr/local/GCC/gcc-4.5.1/lib64
+prepend-path MANPATH /usr/local/GCC/gcc-4.5.1/man
+setenv CC gcc
+setenv CXX g++
+setenv FC gfortran
+setenv F77 gfortran
+setenv F90 gfortran
+setenv F95 gfortran
+#%Module 1.0
+module-whatis "Sets up gcc 4.7.0"
+
+prepend-path PATH /usr/local/GCC/4.7.0/bin
+prepend-path LD_LIBRARY_PATH /usr/local/GCC/4.7.0/lib
+prepend-path LD_LIBRARY_PATH /usr/local/GCC/4.7.0/lib64
+prepend-path MANPATH /usr/local/GCC/4.7.0/man
+setenv CC gcc
+setenv CXX g++
+setenv FC gfortran
+setenv F77 gfortran
+setenv F90 gfortran
+setenv F95 gfortran

genetorrent/.version

+#%Module 1.0
+set ModulesVersion 3.3.4

genetorrent/3.3.4

+#%Module 1.0
+#
+
+module-whatis "Sets up GeneTorrent"
+
+# Define PATHs
+prepend-path LD_LIBRARY_PATH /usr/local/xerces-c-3.0.1-x86_64-linux-gcc-3.4/lib/
+prepend-path LD_INCLUDE_PATH /usr/local/xerces-c-3.0.1-x86_64-linux-gcc-3.4/include/
+#%Module 1.0
+#
+
+module-whatis "Sets up Genome STRiP (Genome STRucture In Populations)"
+
+prepend-path    PATH   /usr/local/R-2.15-64_cluster/bin/:/usr/local/gatk/svtoolkit/bwa
+prepend-path    LD_LIBRARY_PATH /usr/local/GSL/1.15/lib:/usr/local/R-2.15-64_cluster/lib64/R/lib/
+
+#%Module 1.0
+module-whatis "Sets up graphviz v2.28"
+
+# Define PATHs
+
+# The values depend on the machine...
+set hostname [exec /bin/uname -n]
+if { $hostname == "helix.nih.gov" }  {
+  prepend-path PATH /usr/local/graphviz-2.28.0_el6/bin
+  prepend-path LD_LIBRARY_PATH /usr/local/graphviz-2.28.0_el6/lib64
+} else {
+  prepend-path PATH /usr/local/graphviz-2.28.0_el5/bin
+  prepend-path LD_LIBRARY_PATH /usr/local/graphviz-2.28.0_el5/lib64
+}
+#%Module 1.0
+#
+
+module-whatis "Sets up GROMACS 4.5.5"
+
+set ModulesVersion 4.5.5
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up GROMACS 4.5.1"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/openmpi_ib/bin
+prepend-path  PATH          /usr/local/gromacs-4.5.1/bin
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up GROMACS 4.5.3"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/openmpi_ib/bin
+prepend-path  PATH          /usr/local/gromacs-4.5.3/bin
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up GROMACS 4.5.5"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/openmpi_ib/bin
+prepend-path  PATH          /usr/local/GROMACS/4.5.5/bin
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up GROMACS 4.6 Development version"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/GROMACS/4.6-dev/bin
+
+ 		
+#%Module 1.0
+#
+
+# Define prefix so PATH and MANPATH can be updated.
+prepend-path  PATH          /usr/local/hmmer-3.0rc1/bin
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up htseq"
+
+prepend-path PYTHONPATH /usr/local/python-2.7/lib
+prepend-path  PATH   	 /usr/local/python-2.7/bin
+#%Module 1.0
+
+module-whatis "Sets up Integrative Genomics Viewer v2.0.3" 
+set-alias igv /usr/local/apps/IGV/2.0.3/igv.sh
+#%Module 1.0
+
+module-whatis "Sets up Integrative Genomics Viewer v2.0.34" 
+set-alias igv /usr/local/apps/IGV/2.0.34/igv.sh
+#%Module 1.0
+
+module-whatis "Sets up Integrative Genomics Viewer v2.1.17" 
+set-alias igv /usr/local/apps/IGV/2.1.17/igv.sh
+#%Module 1.0
+
+module-whatis "Sets up Integrative Genomics Viewer v2.1.24" 
+set-alias igv /usr/local/apps/IGV/2.1.24/igv.sh
+#%Module 1.0
+
+module-whatis "Sets up Integrative Genomics Viewer v2.1.30" 
+set-alias igv /usr/local/apps/IGV/2.1.30/igv.sh
+#%Module 1.0
+
+module-whatis "Sets up Integrative Genomics Toolkit v2.1.24" 
+set-alias igvtools /usr/local/IGVTools_2.1.24/igvtools
+set-alias igvtools_gui /usr/local/IGVTools_2.1.24/igvtools_gui
+#%Module 1.0
+
+module-whatis "Sets up Integrative Genomics Toolkit v2.1.7" 
+set-alias igvtools /usr/local/IGVTools_2.1.7/igvtools
+set-alias igvtools_gui /usr/local/IGVTools_2.1.7/igvtools_gui
+#%Module 1.0
+#
+
+module-whatis "Sets up Impute, Snptest, Gtool, and QCtool"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/impute
+ 		

inspect/2010.10.12

+#%Module 1.0
+#
+
+module-whatis "Sets up Inspect 2010-10-12"
+
+# Define PATHs
+prepend-path  PATH         /usr/local/Inspect-20101012

inspect/2012.01.09

+#%Module 1.0
+#
+
+module-whatis "Sets up Inspect 2012-01-09"
+
+# Define PATHs
+prepend-path  PATH         /usr/local/Inspect-2012.01.09
+#%Module 1.0
+#
+
+module-whatis "Sets up Lumpy-sv 0.1"
+
+prepend-path  PATH   	 /usr/local/lumpy-sv-0.1/bin
+prepend-path LD_LIBRARY_PATH /usr/local/gsl-1.15/lib
+prepend-path PATH  /usr/local/bedtools-2.17.0/bin/
+#%Module 1.0
+#
+
+module-whatis "Sets up Mach 1.0.12"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/MACH/mach-1.0.12/executables
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up Mach 1.0.17"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/MACH/mach-1.0.17/executables
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up Mach2qtl"
+
+# Define PATHs
+prepend-path  PATH          /usr/local/mach2qtl/executables
+
+ 		
+#%Module 1.0
+#
+
+module-whatis "Sets up macs 1.4.1"
+
+prepend-path PYTHONPATH /usr/local/Python/2.7.2/lib/python2.7/site-packages
+prepend-path  PATH   	 /usr/local/Python/2.7.2/bin
+prepend-path  PATH   	 /usr/local/MACS/MACS-1.4.1/bin
+
+#%Module 1.0
+#
+
+module-whatis "Sets up macs 1.4.2"
+
+prepend-path PYTHONPATH /usr/local/Python/2.7.2/lib/python2.7/site-packages
+prepend-path  PATH   	 /usr/local/Python/2.7.2/bin
+prepend-path  PATH   	 /usr/local/MACS/MACS-1.4.2/bin
+
+#%Module 1.0
+#
+
+module-whatis "Sets up macs 2.0.10"
+
+prepend-path PYTHONPATH /usr/local/Python/2.7.2/lib/python2.7/site-packages
+prepend-path  PATH   	 /usr/local/Python/2.7.2/bin
+prepend-path  PATH   	 /usr/local/MACS/MACS-2.0.10/
+#%Module 1.0
+#
+
+module-whatis "Sets up mapsplice 1.15.2"
+
+prepend-path  PATH   	 /usr/local/MapSplice_1.15.2/bin
+#%Module 1.0
+#
+#  Mathematica  module for use with 'environment-modules' package on helix/biowulf:
+# 
+
+module-whatis "Sets up Mathematica 9 on helix/biowulf cluster"
+
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    # Set aliases for matlab 
+    set-alias "mathematica" "/usr/local/math-8004/bin/mathematica"
+    set-alias "mcc" "/usr/local/math-8004/bin/mcc"
+    set-alias "math" "/usr/local/math-8004/bin/math"
+    set-alias "Mathematica" "/usr/local/math-8004/bin/Mathematica"
+    set-alias "MathematicaScript" "/usr/local/math-8004/MathematicaScript"
+    set-alias "MathKernel" "/usr/local/math-8004/bin/MathKernel"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # Mathematica should not run on the biowulf head node
+       puts stderr "Mathematica sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/math.html for"
+       puts stderr "information on using mathematica on Biowulf."
+       puts stderr " "
+       break
+   } else {
+        set-alias "mathematica" "/usr/local/math-8004/bin/mathematica"
+        set-alias "mcc" "/usr/local/math-8004/bin/mcc"
+        set-alias "math" "/usr/local/math-8004/bin/math"
+        set-alias "Mathematica" "/usr/local/math-8004/bin/Mathematica"
+        set-alias "MathematicaScript" "/usr/local/math-8004/MathematicaScript"
+        set-alias "MathKernel" "/usr/local/math-8004/bin/MathKernel"
+      }
+  }
+
+
+
+#%Module 1.0
+#
+#  Mathematica  module for use with 'environment-modules' package on helix/biowulf:
+# 
+
+module-whatis "Sets up Mathematica 9 on helix/biowulf cluster"
+
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    # Set aliases for matlab 
+    set-alias "mathematica" "/usr/local/math-9000/bin/mathematica"
+    set-alias "mcc" "/usr/local/math-9000/bin/mcc"
+    set-alias "math" "/usr/local/math-9000/bin/math"
+    set-alias "Mathematica" "/usr/local/math-9000/bin/Mathematica"
+    set-alias "MathematicaScript" "/usr/local/math-9000/MathematicaScript"
+    set-alias "MathKernel" "/usr/local/math-9000/bin/MathKernel"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # Mathematica should not run on the biowulf head node
+       puts stderr "Mathematica sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/math.html for"
+       puts stderr "information on using mathematica on Biowulf."
+       puts stderr " "
+       break
+   } else {
+        set-alias "mathematica" "/usr/local/math-9000/bin/mathematica"
+        set-alias "mcc" "/usr/local/math-9000/bin/mcc"
+        set-alias "math" "/usr/local/math-9000/bin/math"
+        set-alias "Mathematica" "/usr/local/math-9000/bin/Mathematica"
+        set-alias "MathematicaScript" "/usr/local/math-9000/MathematicaScript"
+        set-alias "MathKernel" "/usr/local/math-9000/bin/MathKernel"
+      }
+  }
+
+
+
+#%Module 1.0
+#
+#  Matlab  module for use with 'environment-modules' package on helix:
+# 
+
+module-whatis "Sets up Matlab 2006a on helix/biowulf cluster"
+
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    # Set aliases for matlab 
+    set-alias "matlab" "/usr/local/matlab-2006a/bin/matlab -singleCompThread"
+    set-alias "mcc" "/usr/local/matlab-2006a/bin/mcc"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # Matlab should not run on the biowulf head node
+       puts stderr "Matlab sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/matlab.html for"
+       puts stderr "information on using matlab on Biowulf."
+       puts stderr " "
+       break
+   } else {
+       set-alias "matlab" "/usr/local/matlab-2006a/bin/matlab"
+       set-alias "mcc" "/usr/local/matlab-2006a/bin/mcc"       
+      }
+  }
+
+
+
+#%Module 1.0
+#
+#  Matlab  module for use with 'environment-modules' package on helix:
+# 
+
+module-whatis "Sets up Matlab 2011a on helix/biowulf cluster"
+
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    # Set aliases for matlab 
+    set-alias "matlab" "/usr/local/matlab_2011a/bin/matlab -singleCompThread"
+    set-alias "mcc" "/usr/local/matlab_2011a/bin/mcc"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # Matlab should not run on the biowulf head node
+       puts stderr "Matlab sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/matlab.html for"
+       puts stderr "information on using matlab on Biowulf."
+       puts stderr " "
+       break
+   } else {
+       set-alias "matlab" "/usr/local/matlab_2011a/bin/matlab"
+       set-alias "mcc" "/usr/local/matlab_2011a/bin/mcc"       
+      }
+  }
+
+
+
+#%Module 1.0
+#
+#  Matlab  module for use with 'environment-modules' package on helix:
+# 
+
+module-whatis "Sets up Matlab 2011b on helix/biowulf cluster"
+
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    # Set aliases for matlab 
+    set-alias "matlab" "/usr/local/matlab_2011b/bin/matlab -singleCompThread"
+    set-alias "mcc" "/usr/local/matlab_2011b/bin/mcc"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # Matlab should not run on the biowulf head node
+       puts stderr "Matlab sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/matlab.html for"
+       puts stderr "information on using matlab on Biowulf."
+       puts stderr " "
+       break
+   } else {
+       set-alias "matlab" "/usr/local/matlab_2011b/bin/matlab"
+       set-alias "mcc" "/usr/local/matlab_2011b/bin/mcc"       
+      }
+  }
+
+
+
+#%Module 1.0
+#
+#  Matlab  module for use with 'environment-modules' package on helix:
+# 
+
+module-whatis "Sets up Matlab 2012a on helix/biowulf cluster"
+
+
+if { [file exists "/bin/uname"] } {
+  set hostname [exec /bin/uname -n]
+  if { $hostname == "helix.nih.gov" }  {
+    # Set aliases for matlab 
+    set-alias "matlab" "/usr/local/matlab_2012a/bin/matlab -singleCompThread"
+    set-alias "mcc" "/usr/local/matlab_2012a/bin/mcc"
+ } elseif { $hostname == "biowulf.nih.gov" } {
+       # Matlab should not run on the biowulf head node
+       puts stderr "Matlab sessions are not allowed on the Biowulf login node."
+       puts stderr "Please submit a batch job, or allocate an interactive"
+       puts stderr "node. See http://biowulf.nih.gov/apps/matlab.html for"
+       puts stderr "information on using matlab on Biowulf."
+       puts stderr " "
+       break
+   } else {
+       set-alias "matlab" "/usr/local/matlab_2012a/bin/matlab"
+       set-alias "mcc" "/usr/local/matlab_2012a/bin/mcc"