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eXpress
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build
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instructions
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on
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TACC
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Ranger (in the bash shell)
author's
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installation
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instructions:
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http://bio.math.berkeley.edu/eXpress/tutorial.html#install
...
A few of these commands, like "export" are bash specific commands. Rather than make this installation guide a shell independent novel, I'll ask users to either translate those commands to your shell of choice or switch to bash (by typing bash at the command line) before proceeding.
On Ranger and Lonestar, we don't need to install cmake or boost, already have that as a module
Setup environment:
| Code Block |
|---|
module swap $TACC_FAMILY_COMPILER gcc
module load cmake
module load boost
{code}
h5. Download source for eXpress and BamTools (both links are availabe in the |
Download source for eXpress and BamTools (both links are availabe in the "author's
...
installation
...
instructions"
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link
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above)
...
| Code Block |
|---|
wget http://bio.math.berkeley.edu/eXpress/downloads/express-1.1.01/express-1.1.01-src.tgz tar zxvf express-1.1.0-src*.tgz cd ./express*/ # Remember where eXpress unpacked itself export MY_EXPRESS_DIR=`pwd` # Download BamTools from github wget --no-check-certificate https://github.com/downloads/pezmaster31/bamtools/bamtools-1.0.2.tar.gz # extract BamTools into $MY_EXPRESS_DIR then install tar zxvf bamtools-1.0.2*.tar.gz # strip off the version number from the bamtools cddirectory mv ./bamtools*/ # Remember where BamTools unpacked itself ./bamtools/ cd ./bamtools export MY_BAMTOOLS_DIR=`pwd` {code} h5. Build bamtools {code} |
Build bamtools
| Code Block |
|---|
cd $MY_BAMTOOLS_DIR
mkdir build
cd build
cmake ..
make
{code}
h5. Build and Install eXpress
{code} |
Start building eXpress
| Code Block |
|---|
cd $MY_EXPRESS_DIR/src mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=$MY_EXPRESS_DIR ../src {code} \# cmake |
cmake doesn't
...
do
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a
...
good
...
job
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of
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building
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the
...
file
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"$EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt"
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it
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ignores
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the
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links
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needed
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for
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BamTools
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and
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Boost,
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but
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we
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can
...
fix
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that
...
!
This little script is not the prettiest way to do this, but it works as a "cut and paste" way to add what is missing while reusing what we can to make this work on both Ranger and Lonestar. There's probably a better way to do this within cmake.
| Code Block |
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cp ./CMakeFiles/express.dir/bundleslink.otxt CMakeFiles/express.dir/fld.o CMakeFiles/express.dir/fragments.o CMakeFiles/express.dir/main.o CMakeFiles/express.dir/mapparser.o CMakeFiles/express.dir/markovmodel.o CMakeFiles/express.dir/mismatchmodel.o CMakeFiles/express.dir/robertsfilter.o CMakeFiles/express.dir/sequence.o CMakeFiles/express.dir/targets.o CMakeFiles/express.dir/threadsafety.o \-o express \-rdynamic \-Wl,-rpath,/work/01863/benni/express-1.1.0-src/bamtools/lib \-L/work/01863/benni/express-1.1.0-src/bamtools/lib \-lbamtools \-L/opt/apps/gcc4_4/boost/1.48.0/lib \-lboost_filesystem \-lboost_thread \-lboost_system \-lboost_program_options \-lpthread" > $EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt Edit: I want a way to edit this file, not just overwrite it. This is a work in progress: cat link.txt \| sed \link.txt.original cat ./CMakeFiles/express.dir/link.txt.original|sed -r "s/\s+/\n/g" \| awk \-v TACC_BOOST_INC=$TACC_BOOST_INC 'BEGIN -v TACC_BOOST_LIB=$TACC_BOOST_LIB -v MY_BAMTOOLS_DIR=$MY_BAMTOOLS_DIR 'NR==1{print $0;printf "-II%s\n",TACC_BOOST_INC}; NR>1{print};/rdynamic/ {exit}; END{print}' {code} echo "`which c++` -I/opt/apps/gcc4_4/boost/1.48.0/include CMakeFiles/express.dir/biascorrection.o CMakeFiles/express.dir/bundles.o CMakeFiles/express.dir/fld.o CMakeFiles/express.dir/fragments.o CMakeFiles/express.dir/main.o CMakeFiles/express.dir/mapparser.o CMakeFiles/express.dir/markovmodel.o CMakeFiles/express.dir/mismatchmodel.o CMakeFiles/express.dir/robertsfilter.o CMakeFiles/express.dir/sequence.o CMakeFiles/express.dir/targets.o CMakeFiles/express.dir/threadsafety.o -o express -rdynamic -printf "-Wl,-rpath,/work/01863/benni/express-1.1.0-src/bamtools/%s/lib -L/work/01863/benni/express-1.1.0-src/bamtools/L%s/lib -lbamtools -L%s/opt/apps/gcc4_4/boost/1.48.0/liblib/libbamtools.a -L%s -lboost_filesystem -lboost_thread -lboost_system -lboost_program_options -lpthread\n",MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,TACC_BOOST_LIB;}' | tr '\n' ' ' | xargs echo > $EXPRESS_DIR./srcCMakeFiles/build/CMakeFile/express.dir/link.txt {code} |
Finish installing eXpress
| Code Block |
|---|
make CXX_FLAGS="-I$TACC_BOOST_INC \-I../bamtools*/include"-I$MY_BAMTOOLS_DIR/include" make install |
This should put a binary executable called "express" in your $MY_EXPRESS_DIR/bin directory.