Building cufflinks - BenLangmead/jhu-compute GitHub Wiki

Some incomplete instructions on how to build Cufflinks from source on HHPC. I tried this on langmead-login. The instructions don't work because I never got the Eigen3 stuff to compile properly after cufflinks incorporated this pull request. Update: Cole seems to have reverted that change so maybe these work again now.

1. git clone [email protected]:cole-trapnell-lab/cufflinks.git (or git clone [email protected]:BenLangmead/cufflinks.git for my fork)
2. cd cufflinks
3. sh autogen.sh
4. mkdir -p src/libbam/lib src/libbam/include/bam
5. cp /scratch0/langmead-fs1/shared/samtools-0.1.19/*.a src/libbam/lib/
6. cp /scratch0/langmead-fs1/shared/samtools-0.1.19/*.h src/libbam/include/bam/
7. export BOOST_ROOT=/scratch0/langmead-fs1/shared/boost_1_47_0
8. ./configure --prefix=`pwd`/install-root --with-bam=`pwd`/src/libbam