modulefiles / qiime / 1.5.0

#%Module 1.0

module-whatis "Sets up QIIME v1.5.0"

# Define PATHs
prepend-path LD_LIBRARY_PATH /usr/local/tcl_tk/current/lib
prepend-path LD_LIBRARY_PATH /usr/local/SQLite3/3.7.13/lib
prepend-path LD_LIBARAY_PATH /usr/local/GSL/current/lib
prepend-path LD_LIBRARY_PATH /usr/local/QIIME_1.5.0/lib

prepend-path PATH /usr/local/QIIME_1.5.0/bin
prepend-path PATH /usr/local/OpenMPI/current/gnu/eth/bin
prepend-path PATH /usr/local/GSL/current/bin
prepend-path PATH /usr/local/QIIME_1.5.0/apps/microbiomeutil_2010-04-29/ChimeraSlayer
prepend-path PATH /usr/local/QIIME_1.5.0/apps/mothur
prepend-path PATH /usr/local/QIIME_1.5.0/apps/rtax-0.981
prepend-path PATH /usr/local/QIIME_1.5.0/apps/pplacer-v1.1.alpha13r2-Linux-2.6.32
prepend-path PATH /usr/local/QIIME_1.5.0/apps/AmpliconNoiseV1.25/bin
prepend-path PATH /usr/local/QIIME_1.5.0/apps/AmpliconNoiseV1.25/Scripts
prepend-path PATH /usr/local/QIIME_1.5.0/apps/Python-2.7.1/bin
prepend-path PATH /usr/local/QIIME_1.5.0/apps/R-2.12.0/bin
prepend-path PATH /usr/local/QIIME_1.5.0/apps/blast-2.2.22/bin

prepend-path PYTHONPATH /usr/local/QIIME_1.5.0/apps/Python-2.7.1
prepend-path PYTHONPATH /usr/local/QIIME_1.5.0/lib

setenv QIIME_HOME /usr/local/QIIME_1.5.0
setenv QIIME_CONFIG_FP /usr/local/QIIME_1.5.0/qiime_config
setenv RDP_JAR_PATH /usr/local/QIIME_1.5.0/apps/rdp_classifier_2.2/rdp_classifier-2.2.jar
setenv BLASTMAT /usr/local/QIIME_1.5.0/apps/blast-2.2.22/data
setenv PYRO_LOOKUP_FILE /usr/local/QIIME_1.5.0/apps/AmpliconNoiseV1.25/Data/LookUp_E123.dat
setenv SEQ_LOOKUP_FILE /usr/local/QIIME_1.5.0/apps/AmpliconNoiseV1.25/Data/Tran.dat

set-alias figtree "java -Xmx2g -jar /usr/local/QIIME_1.5.0/apps/FigTree_v1.3.1/lib/figtree.jar"

# Fix OMP_NUM_THREADS on helix
if { [file exists "/bin/uname"] } {
  set hostname [exec /bin/uname -n]
  if { $hostname == "helix.nih.gov" }  {
    setenv OMP_NUM_THREADS 4
#  } elseif { $hostname == "biowulf.nih.gov" } {
#    setenv OMP_NUM_THREADS 1
#  } else {
#    setenv OMP_NUM_THREADS 9999
  }
}
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