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samtools-software

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samtools

samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Usage

Show all available versions of samtools:

$ module avail samtools

Load a particular version of samtools:

$ module load samtools/1.6

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/samtools/samtools/releases/download/1.6/samtools-1.6.tar.bz2
$ tar xf samtools-1.6.tar.bz2 
$ cd samtools-1.6
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.6
$ make all all-htslib
$ sudo mkdir /export/apps/samtools/1.6
$ sudo chown aorth /export/apps/samtools/1.6
$ make install install-htslib
$ sudo chown -R root:root /export/apps/samtools/1.6
samtools-software.txt · Last modified: 2017/12/24 14:38 by aorth