samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Show all available versions:
$ module avail samtools
Load one version into your environment and run it:
$ module load samtools/1.15.1 $ samtools
Notes from the sysadmin during installation:
$ 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
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.