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SAMtools

License information

SAMtools is distributed under the MIT/Expat License, a copy of which can be found in the LICENSE file in the SAMtools GitHub repository

Please also note the "Citing" section in the README file in that repository: users are asked to cite a particular paper when usig SAMtools for publications.

After installation of the package and loading of the module, the LICENSE and README files are available in $EBROOTSAMTOOLS/share/licenses/SAMtools (from version 1.17 on).

User-installable modules (and EasyConfigs)

Install with the EasyBuild-user module: 

eb <easyconfig> -r
To access module help after installation and get reminded for which stacks and partitions the module is installed, use module spider SAMtools/<version>.

EasyConfig:

Technical documentation

General information

  • Note that some time ago SAMtools was split in three different packages
    • HTSlib
    • SAMtools itself
    • BCFtools
  • SAMtools contains a number of binaries, a static libraries, several Perl scripts but also two LUA scripts.

EasyConfigs

Version 1.14 for cpeGNU 21.12

  • The EasyConfig is based on the one from the 2021b toolchain of the EasyBuilders repository. HTSlib was added as a dependency though, something that is done in the UAntwerpen version and it does show up in samtools version.

Version 1.15.1 for cpeGNU 21.12

  • Trivial version bump, but we now also unload a few modules that are not needed for compilation, just in case that would solve some problems detected on LUMI.

Version 1.15.1 for CPE 22.06 and 22.08

  • Cleaned up dependencies and removed those that are pulled in through HTSlib.

  • Did another check of the configure options.

Version 1.17 for cpeGNU 22.12

  • Trivial port of the 1.15.1 EasyConfig.

Version 1.18 from CPE 23.09 on

  • Trivial port of the 1.18 EasyConfig.

Archived EasyConfigs

The EasyConfigs below are additonal easyconfigs that are not directly available on the system for installation. Users are advised to use the newer ones and these archived ones are unsupported. They are still provided as a source of information should you need this, e.g., to understand the configuration that was used for earlier work on the system.