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installer_script.tcsh
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installer_script.tcsh
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#!/bin/tcsh -x
### We begin by assuming that you are presently in the parent dir where you'll like all of the profillic-related subdirs to reside. eg
# mkdir profillic-dirs
# cd profillic-dirs
# Note that for installing hmmer-3.1, you need a recent version of the autotools (2.63 or above)
autoconf --version
# If it's not high enough, update it. See the script install-autotools-macosx.sh
## This assumes you already have boost installed. If not, you'll need to follow the installation instructions at the Boost website. You'll do something like this:
# Retrieve boost from http://sourceforge.net/projects/boost/files/boost
# Unpack it. From one dir above it:
# cd boost_1_*
# ./bootstrap.sh
# sudo bjam install
# cd ..
setenv BOOSTLIB /usr/local/lib
setenv BOOSTINC /usr/local/include
#setenv HMMER2 ~/src/profuse-hmmer
#
# uncomment and modify this line if bjam (or the wrong bjam) is on PATH
# alias bjam /usr/bin/bjam
## Download latest seqan (follow instructions at http://trac.seqan.de/wiki/Tutorial/GettingStarted) to get the latest update from the seqan trunk - here's what I do:
svn co http://svn.seqan.de/seqan/trunk seqan-trunk
## Download the latest hmmer snapshot:
svn checkout https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk hmmer
## Get the rest from git:
git clone git://github.com/galosh/profillic.git
git clone git://github.com/galosh/prolific.git
git clone git://github.com/galosh/profuse.git
git clone git://github.com/pedlefsen/HMMoC-BFloat-Algebra.git
git clone git://github.com/galosh/profillic-hmmer
cd HMMoC-BFloat-Algebra/
make
cd ..
cd profillic
ln -s $BOOSTLIB boost-lib
ln -s $BOOSTINC boost-include
ln -s ../prolific
ln -s ../HMMoC-BFloat-Algebra
ln -s ../seqan-trunk
bjam install release
cd ..
cd profuse
ln -s $BOOSTLIB boost-lib
ln -s $BOOSTINC boost-include
ln -s ../prolific
ln -s ../HMMoC-BFloat-Algebra
ln -s ../seqan-trunk
bjam install release
cd ..
cd hmmer
autoconf
./configure
make
cd ..
cd profillic-hmmer
ln -s $BOOSTLIB boost-lib
ln -s $BOOSTINC boost-include
ln -s ../hmmer
ln -s ../seqan-trunk
ln -s ../prolific
ln -s ../HMMoC-BFloat-Algebra
make
cd ..