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cd $MY_BAMTOOLS_DIR mkdir build cd build cmake .. make |
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Start building eXpress
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cd $MY_EXPRESS_DIR mkdir build cd build cmake ../src |
# cmake doesn't do a good job of building the file "$EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt" it ignores the links needed for BamTools and Boost, but we can fix that! echo "/opt/apps/gcc_amd/4.4.5/bin/c++ -I/opt/apps/gcc4_4/boost/1.48.0/include
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.
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mv ./CMakeFiles/express.dir/ |
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link.txt ./CMakeFiles/express.dir/ |
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link.txt.original cat ./CMakeFiles/express.dir/link. |
...
Edit: I want a way to edit this file, not just overwrite it. This is a work in progress:
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cat link.txt 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 ' BEGIN {printf "-I%s\n","TACC_BOOST_INC"}; {print}; /rdynamic/ {exit}; {print}' |
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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 - END {printf "-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%s/lib\n-L%s/lib\n-lbamtools\n-L%s -lboost_filesystem -lboost_thread -lboost_system -lboost_program_options -lpthread\n",MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,TACC_BOOST_LIB;}' \ | tr '\n' ' ' | xargs echo > $EXPRESS_DIR./srcCMakeFiles/build/CMakeFile/express.dir/link.txt |
Finish installing eXpress
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make CXX_FLAGS="-I$TACC_BOOST_INC -I../bamtools*/include" |