ILRI Research Computing

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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.

  * Latest Version: 1.15.1
  * Added: February, 2015
  * Updated: June, 2022
  * Link: http://www.htslib.org

===== Usage =====

Show all available versions:
<code>$ module avail samtools</code>

Load one version into your environment and run it:
<code>$ module load samtools/1.15.1
$ samtools</code>

===== Installation =====
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
$ tar xf samtools-1.15.1.tar.bz2
$ cd samtools-1.15.1
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.15.1 --with-htslib=/export/apps/htslib/1.15.1
$ make
$ sudo mkdir -p /export/apps/samtools/1.15.1
$ sudo chown aorth /export/apps/samtools/1.15.1
$ make install
$ sudo chown -R root:root /export/apps/samtools/1.15.1</code>

This links against htslib/1.15.1, which is installed as a module. As of 1.15.1 this was compiled on CentOS 8 Stream.