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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/1.11
$ samtools


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ tar xf samtools-1.11.tar.bz2
$ cd samtools-1.11
# 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/1.11 --with-htslib=/export/apps/htslib/1.11
$ make
$ sudo mkdir -p /export/apps/samtools/1.11
$ sudo chown aorth /export/apps/samtools/1.11
$ make install
$ sudo chown -R root:root /export/apps/samtools/1.11

This links against htslib/1.11, which is installed as a module.

samtools-software.txt · Last modified: 2021/01/17 10:22 by aorth