#4 Installation:

[Sergey Mitrofanov]

Hi,
about installation bugs..
1. It requires cmake >= 3.3.2 (standart cmake from apt-get in ubuntu 14.04 doesn't fit).
2. I couldn't compile Integrate until I replaced gtest-1.6.0 in sources with https://googletest.googlecode.com/files/gtest-1.7.0.zip ($INTEGRATEDIR/Integrate/build-common/vendor)
3. After "cmake ../Integrate/ -DCMAKE_BUILD_TYPE=release": flags -pthread in 2 files lead to errors during compilation on Linux (on Mac this is ok)
i=$INTEGRATEDIR/INTEGRATE-build
f1=$i/test/CMakeFiles/TestIntegrateLib.dir/link.txt
f2=$i/src/CMakeFiles/integrate-bin.dir/link.txt
mv $f1 ${f1}_orig
mv $f2 ${f2}_orig
cat ${f1}_orig | sed -e "s/-lpthread -lpthread /-pthread /" > $f1
cat ${f2}_orig | sed -e "s/-lpthread -lpthread /-pthread /" > $f2
4. I suppose that "../Integrate/" can be changed to any other installation directory but it is not mentioned anywhere in help.
5. samtools inside sources is rather old.

[Jin]

Hi,

Thank you for sharing this installation solution.

Compiling C++ code on different computers may be slightly different. Older versions of cmake and gtest-1.6.0 worked on my system. However, newer versions maybe better. Line 36 of CMakeLists.txt can also be commented out to avoid gtest and will not affect fusion calling.

Code from samtools is used to read in bam1_t records. Version doesn't matter much here. But newer versions of samtools maybe added to the vendor folder to replace v0.1.19.