Sunday, May 12, 2013

Compiling SamTools

Taken from Cufflinks – Getting Started

For more information, see Compiling SamTools

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

SAMTools (0.1.19)
Step 1: – Download SAMTools

Step 2: – Unpack and compile the SAMTools
# tar -zxvf samtools-0.1.19
# make

Step 3: – Copy the compiled libraries to /usr/local/lib
# cp $SAMTOOLS_HOME/libbam.a /usr/local/lib

Step 4: Copy headers to /usr/local/include
# mkdir /usr/local/include/bam
# cp $SAMTOOLS_HOME/*.h /usr/local/include/bam

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