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 of samtools:
$ module avail samtools
Load a particular version of samtools into your environment and run it:
$ module load samtools/1.13 $ samtools
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2 $ tar xf samtools-1.13.tar.bz2 $ cd samtools-1.13 # install a newer compiler from Red Hat software collections $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ $ scl enable devtoolset-7 bash $ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.13 --with-htslib=/export/apps/htslib/1.13 $ make $ sudo mkdir -p /export/apps/samtools/1.13 $ sudo chown aorth /export/apps/samtools/1.13 $ make install $ sudo chown -R root:root /export/apps/samtools/1.13
This links against htslib/1.13, which is installed as a module.