[91] | 1 | #!/bin/bash |
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| 2 | |
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| 3 | if [ ! -e /etc/debian_version ]; then |
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| 4 | echo "本批次安裝檔目前僅適用 Debian 或 Ubuntu 系列,敬請見諒!!" |
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| 5 | exit 1 |
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| 6 | fi |
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| 7 | |
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[93] | 8 | case "$1" in |
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| 9 | clean) |
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| 10 | sudo rm -rf add_path ape_2.3-1.tar.gz biocLite.R BioConductor.R blast gee_4.13-13.tar.gz GPG-KEY-DRBL lattice_0.17-25.tar.gz mito.nt.gz mpiblast-1.5.0-pio mpiBLAST-1.5.0-pio.tgz mpich2-1.0.8p1 mpich2-1.0.8p1.tar.gz nlme_3.1-92.tar.gz Rmpi_0.5-7.tar.gz torque-2.3.6 torque-2.3.6.tar.gz wwwblast-2.2.20-ia32-linux.tar.gz |
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| 11 | exit 0; |
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| 12 | ;; |
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| 13 | install) |
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| 14 | biocluster_setup |
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| 15 | ;; |
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| 16 | *) |
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| 17 | echo "Usage: $0 [ install | clean ]" |
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| 18 | ;; |
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| 19 | esac |
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| 20 | |
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| 21 | biocluster_setup() |
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| 22 | { |
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[91] | 23 | ##################################################################### |
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| 24 | # 以下為基本程式設計與生資相關自由軟體 |
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| 25 | ##################################################################### |
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| 26 | ######## |
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| 27 | # 安裝基本程式語言編譯環境 |
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| 28 | ######## |
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| 29 | sudo apt-get -y install gcc g++ make autoconf build-essential |
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| 30 | ######## |
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| 31 | # 安裝 JDK 6 編譯環境 |
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| 32 | ######## |
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| 33 | sudo apt-get -y install sun-java6-jdk |
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| 34 | ######## |
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| 35 | # 安裝 GNU R 相關套件 |
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| 36 | # (去除 rjava 與 rmpi 套件, 因為 rmpi 必須特別設定成使用 mpich2 ) |
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| 37 | ######## |
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| 38 | sudo apt-get -y install r-base |
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| 39 | sudo apt-get -y install `apt-cache search --names-only "^r-cran" | awk '{ print $1 }' | grep -v "r-cran-rjava" | grep -v "r-cran-rmpi" ` |
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| 40 | ######## |
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| 41 | # 安裝 GNU R BioConductor 套件 |
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| 42 | ######## |
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| 43 | if [ ! -e biocLite.R ]; then |
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| 44 | sudo wget http://www.bioconductor.org/biocLite.R |
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| 45 | fi |
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| 46 | if [ ! -e BioConductor.R ]; then |
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| 47 | cat > BioConductor.R << EOF |
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| 48 | source(file="$(pwd)/biocLite.R") |
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| 49 | biocLite() |
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| 50 | EOF |
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| 51 | sudo R --no-save < BioConductor.R |
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| 52 | fi |
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| 53 | ######## |
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| 54 | # 安裝 GNU R ape 套件 |
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| 55 | ######## |
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| 56 | sudo apt-get -f install libc6-dev g77 gfortran liblapack-dev |
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| 57 | if [ ! -e gee_4.13-13.tar.gz ]; then |
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| 58 | wget http://cran.r-project.org/src/contrib/gee_4.13-13.tar.gz |
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| 59 | sudo R CMD INSTALL gee_4.13-13.tar.gz |
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| 60 | fi |
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| 61 | if [ ! -e nlme_3.1-92.tar.gz ]; then |
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| 62 | wget http://cran.r-project.org/src/contrib/nlme_3.1-92.tar.gz |
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| 63 | sudo R CMD INSTALL nlme_3.1-92.tar.gz |
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| 64 | fi |
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| 65 | if [ ! -e lattice_0.17-25.tar.gz ]; then |
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| 66 | wget http://cran.r-project.org/src/contrib/lattice_0.17-25.tar.gz |
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| 67 | sudo R CMD INSTALL lattice_0.17-25.tar.gz |
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| 68 | fi |
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| 69 | if [ ! -e ape_2.3-1.tar.gz ]; then |
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| 70 | wget http://cran.r-project.org/src/contrib/ape_2.3-1.tar.gz |
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| 71 | sudo R CMD INSTALL ape_2.3-1.tar.gz |
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| 72 | fi |
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| 73 | ##################################################################### |
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| 74 | # 以下為叢集環境的需求 |
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| 75 | ##################################################################### |
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| 76 | ######## |
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| 77 | # 安裝 MPICH2 |
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| 78 | ######## |
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| 79 | if [ ! -e mpich2-1.0.8p1.tar.gz ]; then |
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| 80 | wget http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.0.8p1/mpich2-1.0.8p1.tar.gz |
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| 81 | tar zxvf mpich2-1.0.8p1.tar.gz |
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| 82 | cd mpich2-1.0.8p1 |
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| 83 | ./configure CFLAGS="-fPIC" CXXFLAGS="-fPIC" FFLAGS="-fPIC" prefix=/opt/mpich2 |
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| 84 | sudo make |
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| 85 | sudo make install |
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| 86 | cd .. |
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| 87 | fi |
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| 88 | ######## |
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| 89 | # 安裝 openPBS / torque |
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| 90 | ######## |
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| 91 | if [ ! -e torque-2.3.6.tar.gz ]; then |
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| 92 | wget wget http://www.clusterresources.com/downloads/torque/torque-2.3.6.tar.gz |
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| 93 | tar zxvf torque-2.3.6.tar.gz |
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| 94 | cd torque-2.3.6/ |
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| 95 | ./configure --prefix=/opt/torque |
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| 96 | sudo make |
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| 97 | sudo make install |
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| 98 | sudo /opt/torque/sbin/pbs_server -t create |
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| 99 | echo "$(hostname)" > nodes |
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| 100 | sudo mv nodes /var/spool/torque/server_priv/nodes |
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| 101 | echo "$(hostname)" > server_name |
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| 102 | sudo mv server_name /var/spool/torque/server_name |
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| 103 | cat > torque_conf << EOF |
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| 104 | create queue batch |
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| 105 | set queue batch queue_type = Execution |
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| 106 | set queue batch started = True |
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| 107 | set queue batch enabled = True |
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| 108 | set server default_queue = batch |
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| 109 | set server resources_default.nodes = 1 |
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| 110 | set server scheduling = True |
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| 111 | EOF |
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| 112 | sudo /opt/torque/bin/qmgr < torque_conf |
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| 113 | cat >> config << EOF |
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| 114 | \$pbsserver $(hostname) |
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| 115 | \$logevent 255 |
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| 116 | EOF |
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| 117 | sudo mv config /var/spool/torque/mom_priv/jobs/config |
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| 118 | sudo /opt/torque/bin/qterm -t quick |
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| 119 | sudo /opt/torque/sbin/pbs_server |
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| 120 | sudo /opt/torque/sbin/pbs_sched |
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| 121 | sudo /opt/torque/sbin/pbs_mom |
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| 122 | sudo /opt/torque/bin/pbsnodes -a |
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| 123 | cd .. |
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| 124 | fi |
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| 125 | |
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| 126 | ######## |
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| 127 | # 安裝 Lustre |
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| 128 | ######## |
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| 129 | if [ ! -e /etc/apt/sources.list.d/lustre.list ]; then |
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| 130 | sudo echo "deb http://www.pdsi-scidac.org/repository/debian testing main" > lustre.list |
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| 131 | sudo mv lustre.list /etc/apt/sources.list.d/lustre.list |
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| 132 | sudo apt-get update |
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| 133 | sudo apt-get -y --force-yes install pdsi-scidac-keyring |
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| 134 | sudo apt-get -y install linux-image-2.6.22.19-lustre-686 lustre-modules-2.6.22.19-lustre-686 lustre-utils |
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| 135 | fi |
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| 136 | ##################################################################### |
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| 137 | # 以下為叢集版本的生資相關軟體 |
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| 138 | ##################################################################### |
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| 139 | ######## |
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| 140 | # 安裝 Rmpi |
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| 141 | ######## |
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| 142 | if [ ! -e Rmpi_0.5-7.tar.gz ]; then |
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| 143 | wget http://www.stats.uwo.ca/faculty/yu/Rmpi/download/linux/Rmpi_0.5-7.tar.gz |
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| 144 | sudo R CMD INSTALL Rmpi_0.5-7.tar.gz --configure-args=--with-mpi=/opt/mpich2 |
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| 145 | fi |
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| 146 | ######## |
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| 147 | # 安裝 mpiBLAST |
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| 148 | # 參考 http://debianclusters.cs.uni.edu/index.php/Installing_mpiBLAST |
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| 149 | ######## |
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| 150 | sudo apt-get install csh |
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| 151 | if [ ! -e mpiBLAST-1.5.0-pio.tgz ]; then |
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| 152 | wget http://www.mpiblast.org/downloads/files/mpiBLAST-1.5.0-pio.tgz |
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| 153 | tar zxvf mpiBLAST-1.5.0-pio.tgz |
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| 154 | cd mpiblast-1.5.0-pio |
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| 155 | ./ncbi/make/makedis.csh 2>&1|tee out.makedis.txt |
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| 156 | ./ncbi/make/makedis.csh 2>&1|tee out.makedis.txt |
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| 157 | ./ncbi/make/makedis.csh 2>&1|tee out.makedis.txt |
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| 158 | ./configure --prefix=/opt/mpiblast --with-mpi=/opt/mpich2 --with-ncbi=`pwd`/ncbi --enable-MPI_Alloc_mem |
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| 159 | sudo make |
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| 160 | sudo make install |
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| 161 | cd .. |
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| 162 | fi |
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[92] | 163 | |
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[93] | 164 | if [ ! -e mito.nt.gz ]; then |
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| 165 | wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/mito.nt.gz |
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| 166 | fi |
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[92] | 167 | |
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[93] | 168 | if [ ! -e add_path ]; then |
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| 169 | cat > add_path << EOF |
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[92] | 170 | echo "export PATH=\\\$PATH:/opt/torque/bin:/opt/mpich2/bin:/opt/mpiblast/bin" >> /etc/profile |
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| 171 | EOF |
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[93] | 172 | sudo sh add_path |
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| 173 | fi |
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[91] | 174 | ##################################################################### |
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| 175 | # 電腦叢集的網頁監控機制 |
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| 176 | ##################################################################### |
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| 177 | ######## |
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| 178 | # 安裝 wwwBLAST |
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| 179 | ######## |
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| 180 | if [ ! -e wwwblast-2.2.20-ia32-linux.tar.gz ]; then |
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| 181 | wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/wwwblast-2.2.20-ia32-linux.tar.gz |
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| 182 | tar zxvf wwwblast-2.2.20-ia32-linux.tar.gz |
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| 183 | fi |
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[92] | 184 | ##################################################################### |
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| 185 | # 安裝 DRBL |
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| 186 | ##################################################################### |
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| 187 | if [ ! -e GPG-KEY-DRBL ]; then |
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| 188 | wget http://drbl.nchc.org.tw/GPG-KEY-DRBL |
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| 189 | sudo apt-key add GPG-KEY-DRBL |
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| 190 | echo "deb http://free.nchc.org.tw/drbl-core drbl stable" > drbl.list |
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| 191 | sudo mv drbl.list /etc/apt/sources.list.d/ |
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| 192 | sudo apt-get update |
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| 193 | sudo apt-get install drbl |
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| 194 | sudo /opt/drbl/sbin/drblsrv -i |
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| 195 | sudo /opt/drbl/sbin/drblpush -i |
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| 196 | fi |
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[93] | 197 | } |
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