D*******e
发帖数: 157 | 1 版上有没有会用featureBit program (from ucsc genome browser)的同学。最近要
collapse 几个annotation file，但是看晕了头也不知道怎么安装。 | y****u
发帖数: 57 | 2 Save below into file like install_kentsrc.sh, chmod to 755, and run it.
Tested under Linux Ubuntu 10.10.
======
#!/bin/bash
#run 'uname -m' to check your MACHTYPE
export MACHTYPE=x86_64
#run 'mysql_config --include' to check your MYSQLINC
export MYSQLINC='/usr/include/mysql'
#run 'mysql_config --libs' to check your MYSQLLIBS
export MYSQLLIBS='-Wl,-Bsymbolic-functions -rdynamic -L/usr/lib/mysql -
lmysqlclient'
# download or update kent source package.
SOFTDIR=${HOME}/tests
cd $SOFTDIR
if [ ! -d kent ]; then
git clone git://genome-source.cse.ucsc.edu/kent.git
cd kent/
git checkout -t -b beta origin/beta #Track the beta branch at UCSC
repository
else
cd kent/
git pull # update
fi
KENT=${SOFTDIR}/kent
KENTSRC=${KENT}/src
# directory in which programs will be.
mkdir -p ${HOME}/bin
mkdir -p ${HOME}/bin/${MACHTYPE}
cd ${KENTSRC}
cd lib/; make clean; make; cd ${KENTSRC}
cd jkOwnLib/; make clean; make; cd ${KENTSRC}
cd utils/; make clean; make alpha; cd ${KENTSRC}
cd utils/stringify; make; cd ${KENTSRC}
cd hg/lib/; make clean; make; cd ${KENTSRC}
# install any ohter program
cd hg/featureBits/; make; cd ${KENTSRC} |
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