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idot/build tophat

Created July 12, 2011 14:35
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build tophat in own folder
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build tophat
#similar to brentp http://biostar.stackexchange.com/questions/4885/installation-of-tophat-1-1-4
* in samtools download mkdir lib include/bam bin
* cp libbam.a lib; *.h include/bam ; samtools bin
tophat:
./configure --with-bam=/path/to/samtools/samtools-0.1.13 --prefix /path/to/tophat/checkout/tophat/tophat.git
make && make install
will create tophat binaries in tophat.git/bin
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