samtools-software
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Table of Contents
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: 1.11
- Added: February, 2015
- Updated: January, 2021
- Link: http://www.htslib.org
Usage
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
Installation
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 $ 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.1610878954.txt.gz · Last modified: 2021/01/17 10:22 by aorth