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Installation notes for samtools-devel version 0.1.19 / bcftools version 0.2.0-rc5-60

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The devel version was needed for GBrowse. It was not available with apt-get, needed to install from source.

Prerequisites

Installation

This program is installed from source, even though it is available in repositories, because other programs may need the header files or libraries

  1. $ ver="0.1.19"
  2. $ cd /programinstallers/
  3. $ wget -N http://downloads.sourceforge.net/project/samtools/samtools/$ver/samtools-$ver.tar.bz2
  4. $ tar -jxvf samtools-$ver.tar.bz2
  5. $ cd samtools-$ver/
  6. Change to be compatible with GBrowse Bio::DB::Sam Perl module install later
    $ nano Makefile
    Edit CFLAGS line to read:
    CFLAGS=         -g -Wall -O2 -fPIC
  7. $ make
  8. Installation must be done manually. The apt-get version is in /usr/bin/, which is later in the PATH than /usr/local/bin, so leave it there and install like so:
    Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to a location you want (e.g. a directory in your $PATH). You may also copy `samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such that the `man' command may find the manual.

    $ cp -puv samtools /usr/local/bin/
  9. $ cp -puv bcftools/vcfutils.pl bcftools/bcftools /usr/local/bin/
  10. $ cp -puv misc/md5sum-lite misc/maq2sam-short misc/maq2sam-long misc/ace2sam misc/wgsim misc/bamcheck /usr/local/bin/
  11. $ chmod 664 samtools.1 && gzip samtools.1 && sudo cp -puv samtools.1.gz /usr/share/man/man1/
    There was no bcftools/bcftools.1 file
  12. If necessary, create this directory
    $ sudo mkdir /usr/lib/samtools/
  13. $ sudo cp -puv *.h bcftools/*.h /usr/lib/samtools/
  14. $ sudo cp -puv *.a bcftools/*.a /usr/lib/samtools/
  15. Cleanup
    $ cd ..
  16. $ rm samtools-$ver -rf