Index: /drbl-biocluster/BioCluster_Setup.sh
===================================================================
--- /drbl-biocluster/BioCluster_Setup.sh	(revision 91)
+++ /drbl-biocluster/BioCluster_Setup.sh	(revision 91)
@@ -0,0 +1,157 @@
+#!/bin/bash
+
+if [ ! -e /etc/debian_version ]; then
+  echo "本批次安裝檔目前僅適用 Debian 或 Ubuntu 系列，敬請見諒!!"
+  exit 1
+fi
+
+#####################################################################
+# 以下為基本程式設計與生資相關自由軟體
+#####################################################################
+########
+# 安裝基本程式語言編譯環境
+########
+sudo apt-get -y install gcc g++ make autoconf build-essential
+########
+# 安裝 JDK 6 編譯環境
+########
+sudo apt-get -y install sun-java6-jdk
+########
+# 安裝 GNU R 相關套件
+# (去除 rjava 與 rmpi 套件, 因為 rmpi 必須特別設定成使用 mpich2 )
+########
+sudo apt-get -y install r-base
+sudo apt-get -y install `apt-cache search --names-only "^r-cran" | awk '{ print $1 }' | grep -v "r-cran-rjava" | grep -v "r-cran-rmpi" `
+########
+# 安裝 GNU R BioConductor 套件
+########
+if [ ! -e biocLite.R ]; then
+  sudo wget http://www.bioconductor.org/biocLite.R
+fi
+if [ ! -e BioConductor.R ]; then
+  cat > BioConductor.R << EOF
+source(file="$(pwd)/biocLite.R")
+biocLite()
+EOF
+  sudo R --no-save < BioConductor.R
+fi
+########
+# 安裝 GNU R ape 套件
+########
+sudo apt-get -f install libc6-dev g77 gfortran liblapack-dev
+if [ ! -e gee_4.13-13.tar.gz ]; then
+  wget http://cran.r-project.org/src/contrib/gee_4.13-13.tar.gz
+  sudo R CMD INSTALL gee_4.13-13.tar.gz
+fi
+if [ ! -e nlme_3.1-92.tar.gz ]; then
+  wget http://cran.r-project.org/src/contrib/nlme_3.1-92.tar.gz
+  sudo R CMD INSTALL nlme_3.1-92.tar.gz
+fi
+if [ ! -e lattice_0.17-25.tar.gz ]; then
+  wget http://cran.r-project.org/src/contrib/lattice_0.17-25.tar.gz
+  sudo R CMD INSTALL lattice_0.17-25.tar.gz
+fi
+if [ ! -e ape_2.3-1.tar.gz ]; then
+  wget http://cran.r-project.org/src/contrib/ape_2.3-1.tar.gz
+  sudo R CMD INSTALL ape_2.3-1.tar.gz
+fi
+#####################################################################
+# 以下為叢集環境的需求
+#####################################################################
+########
+# 安裝 MPICH2
+########
+if [ ! -e mpich2-1.0.8p1.tar.gz ]; then
+  wget http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.0.8p1/mpich2-1.0.8p1.tar.gz
+  tar zxvf mpich2-1.0.8p1.tar.gz
+  cd mpich2-1.0.8p1
+  ./configure CFLAGS="-fPIC" CXXFLAGS="-fPIC" FFLAGS="-fPIC" prefix=/opt/mpich2
+  sudo make
+  sudo make install
+  cd ..
+fi
+########
+# 安裝 openPBS / torque
+########
+if [ ! -e torque-2.3.6.tar.gz ]; then
+  wget wget http://www.clusterresources.com/downloads/torque/torque-2.3.6.tar.gz
+  tar zxvf torque-2.3.6.tar.gz
+  cd torque-2.3.6/
+  ./configure --prefix=/opt/torque
+  sudo make
+  sudo make install
+  sudo /opt/torque/sbin/pbs_server -t create
+  echo "$(hostname)" > nodes
+  sudo mv nodes /var/spool/torque/server_priv/nodes
+  echo "$(hostname)" > server_name
+  sudo mv server_name /var/spool/torque/server_name
+  cat > torque_conf << EOF
+create queue batch
+set queue batch queue_type = Execution
+set queue batch started = True
+set queue batch enabled = True
+set server default_queue = batch
+set server resources_default.nodes = 1
+set server scheduling = True
+EOF
+  sudo /opt/torque/bin/qmgr < torque_conf
+  cat >> config << EOF
+\$pbsserver    $(hostname)
+\$logevent     255
+EOF
+  sudo mv config /var/spool/torque/mom_priv/jobs/config
+  sudo /opt/torque/bin/qterm -t quick
+  sudo /opt/torque/sbin/pbs_server
+  sudo /opt/torque/sbin/pbs_sched
+  sudo /opt/torque/sbin/pbs_mom
+  sudo /opt/torque/bin/pbsnodes -a
+  cd ..
+fi
+
+########
+# 安裝 Lustre
+########
+if [ ! -e /etc/apt/sources.list.d/lustre.list ]; then
+  sudo echo "deb http://www.pdsi-scidac.org/repository/debian testing main" > lustre.list
+  sudo mv lustre.list /etc/apt/sources.list.d/lustre.list
+  sudo apt-get update
+  sudo apt-get -y --force-yes install pdsi-scidac-keyring
+  sudo apt-get -y install linux-image-2.6.22.19-lustre-686 lustre-modules-2.6.22.19-lustre-686 lustre-utils 
+fi
+#####################################################################
+# 以下為叢集版本的生資相關軟體
+#####################################################################
+########
+# 安裝 Rmpi
+########
+if [ ! -e Rmpi_0.5-7.tar.gz ]; then
+  wget http://www.stats.uwo.ca/faculty/yu/Rmpi/download/linux/Rmpi_0.5-7.tar.gz
+  sudo R CMD INSTALL Rmpi_0.5-7.tar.gz --configure-args=--with-mpi=/opt/mpich2
+fi
+########
+# 安裝 mpiBLAST
+# 參考 http://debianclusters.cs.uni.edu/index.php/Installing_mpiBLAST
+########
+sudo apt-get install csh
+if [ ! -e mpiBLAST-1.5.0-pio.tgz ]; then
+  wget http://www.mpiblast.org/downloads/files/mpiBLAST-1.5.0-pio.tgz
+  tar zxvf mpiBLAST-1.5.0-pio.tgz
+  cd mpiblast-1.5.0-pio
+  ./ncbi/make/makedis.csh 2>&1|tee out.makedis.txt
+  ./ncbi/make/makedis.csh 2>&1|tee out.makedis.txt
+  ./ncbi/make/makedis.csh 2>&1|tee out.makedis.txt
+  ./configure --prefix=/opt/mpiblast --with-mpi=/opt/mpich2 --with-ncbi=`pwd`/ncbi --enable-MPI_Alloc_mem
+  sudo make
+  sudo make install
+  cd ..
+fi
+#####################################################################
+# 電腦叢集的網頁監控機制
+#####################################################################
+########
+# 安裝 wwwBLAST
+########
+if [ ! -e wwwblast-2.2.20-ia32-linux.tar.gz ]; then
+  wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/wwwblast-2.2.20-ia32-linux.tar.gz
+  tar zxvf wwwblast-2.2.20-ia32-linux.tar.gz
+fi