This page was last updated on Tuesday, 16-Feb-2016 11:14:02 CST

Installation notes for Pindel version 0.2.5b8, 20151210

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Prerequisites

• Samtools version 1.x development version. See samtools install notes

Installation

1. $ cd /programinstallers/
2. $ git clone git://github.com/genome/pindel.git
3. $ cd pindel
4. Note that Samtools version 1.x is installed in a non-default location to allow Samtools version 0.x to remain installed
   $ ./INSTALL /usr/local/bin/samtools1/include
   but the first time we get an error
   …
   /usr/bin/ld: cannot find -lhts
   …
5. We need to edit the Makefile.local file that was generated to specify where the hts library is located
   $ nano Makefile.local
   …
   HTSLIB_CPPFLAGS=-I/usr/local/bin/samtools1/include
   #HTSLIB_LDFLAGS=-L/usr/local/bin/samtools1/include/ -Wl,-rpath /usr/local/bin/samtools1/include/
   HTSLIB_LDFLAGS=-L/usr/local/bin/samtools1/lib/ -Wl,-rpath /usr/local/bin/samtools1/lib/
   …
6. $ make
7. Install
   $ cp -puv Adaptor.pm bam2pindel.pl src/pindel src/pindel2vcf src/sam2pindel /usr/local/bin/
   

   `Adaptor.pm' -> `/usr/local/bin/Adaptor.pm'
   `bam2pindel.pl' -> `/usr/local/bin/bam2pindel.pl'
   `pindel' -> `/usr/local/bin/pindel'
   `pindel2vcf' -> `/usr/local/bin/pindel2vcf'
   `sam2pindel' -> `/usr/local/bin/sam2pindel'