This page was last updated on Saturday, 12-Nov-2016 09:23:30 CST
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
- ncurses
- $ sudo apt-get install libncurses5-dev
Installation
This program is installed from source, even though it is available in repositories,
because other programs may need the header files or libraries
- $ ver="0.1.19"
- $ cd /programinstallers/
- $ wget -N http://downloads.sourceforge.net/project/samtools/samtools/$ver/samtools-$ver.tar.bz2
- $ tar -jxvf samtools-$ver.tar.bz2
- $ cd samtools-$ver/
- 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
- $ make
- 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/
- $ cp -puv bcftools/vcfutils.pl bcftools/bcftools /usr/local/bin/
- $ cp -puv misc/md5sum-lite misc/maq2sam-short misc/maq2sam-long misc/ace2sam misc/wgsim misc/bamcheck /usr/local/bin/
- $ chmod 664 samtools.1 && gzip samtools.1 && sudo cp -puv samtools.1.gz /usr/share/man/man1/
There was no bcftools/bcftools.1 file
- If necessary, create this directory
$ sudo mkdir /usr/lib/samtools/
- $ sudo cp -puv *.h bcftools/*.h /usr/lib/samtools/
- $ sudo cp -puv *.a bcftools/*.a /usr/lib/samtools/
- Cleanup
$ cd ..
- $ rm samtools-$ver -rf