This page was last updated on Wednesday, 09-Nov-2016 21:22:48 CST

Installation notes for VCFtools version 0.1.14 Oct. 11, 2015

vcftools home Page

bcftools/htslib home page

Prerequisites

autoconf
$ sudo apt-get install autoconf

pkg-config
$ sudo apt-get install pkg-config

Installation

1. $ ver="0.1.14" .tarball-version on github has version number
2. $ cd /programinstallers/
3. $ wget https://github.com/vcftools/vcftools/archive/master.zip
4. $ mv master.zip vcftools_$ver.zip
5. $ unzip vcftools_$ver.zip
6. $ cd vcftools-master
7. $ ./autogen.sh
8. $ ./configure
9. $ make
10. Manual install
    $ mkdir /usr/local/bin/vcftools_$ver
11. $ cp -puv src/perl/* src/cpp/vcftools /usr/local/bin/vcftools_$ver/
12. $ rm /usr/local/bin/vcftools_$ver/Make*
13. $ chmod +x /usr/local/bin/vcftools_$ver/*
14. Make a version-independent symlink
    $ ln -s /usr/local/bin/vcftools_$ver /usr/local/bin/vcftools
15. Fix so that perl modules can be located
    $ cd /usr/local/bin
16. $ ln -s /usr/local/bin/vcftools vcftools/perl
17. Add to default PATH
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/vcftools"
    ...
    export PERL5LIB="$PERL5LIB:/usr/local/bin/vcftools"
    ...
18. Cleanup
    $ cd /programinstallers
19. $ rm vcftools-master -rf
20. To install the bcftools/htslib VCF commands
    $ git clone git://github.com/samtools/htslib.git htslib
21. $ git clone git://github.com/samtools/bcftools.git bcftools
22. $ cd htslib; git pull; cd .. (only if updating)
23. $ cd bcftools; git pull; cd .. (only if updating)
24. $ cd bcftools
25. $ make
26. $ make test
27. Install. Samtools also has a program called bcftools, so make this version use a different name than the samtools version
    $ cp -puv bcftools /usr/local/bin/bcftools2
28. Cleanup
    $ cd ..
29. $ rm htslib bcftools -rf