This page was last updated on Tuesday, 25-Jun-2019 16:03:28 CDT

Installation notes for samtools version 1.2, BCFtools version 1.2, and HTSlib version 1.2.1

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Prerequisites

None

Installation

1. $ cd /programinstallers/
2. $ vers="1.2"; verb="1.2"; verh="1.2.1"
3. $ wget -N https://github.com/samtools/htslib/releases/download/$verh/htslib-$verh.tar.bz2
4. $ wget -N https://github.com/samtools/samtools/releases/download/$vers/samtools-$vers.tar.bz2
5. $ wget -N https://github.com/samtools/bcftools/releases/download/$verb/bcftools-$verb.tar.bz2
6. $ tar -jxvf htslib-$verh.tar.bz2 && tar -jxvf samtools-$vers.tar.bz2 && tar -jxvf bcftools-$verb.tar.bz2
7. To allow coexistence with version 0.xx series of samtools, version 1.x files will be installed in a separate location
   $ mkdir /usr/local/bin/samtools1
8. $ cd htslib-$verh
9. $ make
10. $ make prefix=/usr/local/bin/samtools1 install
11. $ cd ../samtools-$vers
12. $ make
13. $ make prefix=/usr/local/bin/samtools1 install
14. $ cd ../bcftools-$verb
15. $ make
16. $ make prefix=/usr/local/bin/samtools1 install
17. $ cd ..
18. Cleanup
    $ rm samtools-$vers bcftools-$verb htslib-$verh -rf
19. Plugin configuration
    $ sudo nano /etc/profile
    …
    export BCFTOOLS_PLUGINS=/usr/local/bin/samtools1/libexec/bcftools
    …