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| 1 | +#! /bin/bash |
| 2 | + |
| 3 | +set -xe |
| 4 | + |
| 5 | +if [[ -z "${TMPDIR}" ]]; then |
| 6 | + TMPDIR=/tmp |
| 7 | +fi |
| 8 | + |
| 9 | +set -u |
| 10 | + |
| 11 | +if [ "$#" -lt "1" ] ; then |
| 12 | + echo "Please provide an installation path such as /opt/ICGC" |
| 13 | + exit 1 |
| 14 | +fi |
| 15 | + |
| 16 | +# get path to this script |
| 17 | +SCRIPT_PATH=`dirname $0`; |
| 18 | +SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)` |
| 19 | + |
| 20 | +# get the location to install to |
| 21 | +INST_PATH=$1 |
| 22 | +mkdir -p $1 |
| 23 | +INST_PATH=`(cd $1 && pwd)` |
| 24 | +echo $INST_PATH |
| 25 | + |
| 26 | +# get current directory |
| 27 | +INIT_DIR=`pwd` |
| 28 | + |
| 29 | +CPU=`grep -c ^processor /proc/cpuinfo` |
| 30 | +if [ $? -eq 0 ]; then |
| 31 | + if [ "$CPU" -gt "6" ]; then |
| 32 | + CPU=6 |
| 33 | + fi |
| 34 | +else |
| 35 | + CPU=1 |
| 36 | +fi |
| 37 | +echo "Max compilation CPUs set to $CPU" |
| 38 | + |
| 39 | +SETUP_DIR=$INIT_DIR/install_tmp |
| 40 | +mkdir -p $SETUP_DIR/distro # don't delete the actual distro directory until the very end |
| 41 | +mkdir -p $INST_PATH/bin |
| 42 | +cd $SETUP_DIR |
| 43 | + |
| 44 | +# make sure tools installed can see the install loc of libraries |
| 45 | +set +u |
| 46 | +export LD_LIBRARY_PATH=`echo $INST_PATH/lib:$LD_LIBRARY_PATH | perl -pe 's/:\$//;'` |
| 47 | +export PATH=`echo $INST_PATH/bin:$PATH | perl -pe 's/:\$//;'` |
| 48 | +export MANPATH=`echo $INST_PATH/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/:\$//;'` |
| 49 | +export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'` |
| 50 | +set -u |
| 51 | + |
| 52 | +# Rlibs |
| 53 | +if [ ! -e $SETUP_DIR/Rlib.success ]; then |
| 54 | + cd $INIT_DIR/Rsupport |
| 55 | + ./setupR.sh $OPT |
| 56 | + touch $SETUP_DIR/Rlib.success |
| 57 | +fi |
| 58 | + |
| 59 | +## install included distro for velvet |
| 60 | +if [ ! -e $SETUP_DIR/velvet.success ]; then |
| 61 | + cd $INIT_DIR |
| 62 | + cd $INIT_DIR/distros |
| 63 | + tar -mzxf velvet_1.2.10.tgz |
| 64 | + cd velvet_1.2.10 |
| 65 | + make MAXKMERLENGTH=95 velveth velvetg |
| 66 | + mv velveth $INST_PATH/bin/velvet95h |
| 67 | + mv velvetg $INST_PATH/bin/velvet95g |
| 68 | + make clean |
| 69 | + make velveth velvetg # don't do multi-threaded make |
| 70 | + mv velveth $INST_PATH/bin/velvet31h |
| 71 | + mv velvetg $INST_PATH/bin/velvet31g |
| 72 | + ln -fs $INST_PATH/bin/velvet95h $INST_PATH/bin/velveth |
| 73 | + ln -fs $INST_PATH/bin/velvet95g $INST_PATH/bin/velvetg |
| 74 | + cd $INIT_DIR |
| 75 | + rm -rf $INIT_DIR/distros/velvet_1.2.10 |
| 76 | + touch $SETUP_DIR/velvet.success |
| 77 | +fi |
| 78 | + |
| 79 | +# cleanup all junk |
| 80 | +rm -rf $SETUP_DIR |
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