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HTSlib

License information

Source files of HTSlib are covered by different licesnes. Some source files are covered by the MIT/Expat license while others are covered by a modifed 3-clause BSD license.

See the LICENSE file in the GitHub repository for complete information.

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

After installation of the package and loading of the module, the LICENSE and README files are available in $EBROOTHTSLIB/share/licenses/HTSlib (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 HTSlib/<version>.

EasyConfig:

Technical documentation

General information

  • HTSlib is the underlying library of SAMtools
  • The build process creates three binaries, a shared and a static library.
  • HTSlib dependencies:
    • zlib
    • libdeflate can substitute for zlib for zlib compression
    • libbz2
    • liblzma
    • libcurl: Optional but recommended for network access.
    • libcrypto: We always take this one from the OS to ensure that security patches are applied.

EasyBuild

Version 1.14 for cpeGNU 21.12

  • We started from the EasyBuilders EasyConfig for the 2021b common toolchains but added documentation from UAntwerpen.

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 cpeGNU 22.06 and 22.08

  • Switched from zlib to libdeflate for zlib compression based on a recommendation on the SAMtools documentation page "A comparison of zlib implementations".

    The zlib module still comes in as a dependency through other libraries, but this does not seem to be a problem as the configure script indicates the APIs are different (looking at the tests).

  • Checked the configure options, leading to a new configopts line. S3 and Google Cloud Integration were not tested, so it is not clear if this fully works or not.

Version 1.17 for cpeGNU 22.12

  • Trivial port of the EasyConfig for 1.15.1.

  • Some reworking for our system to update versions of dependencies.

  • Some reworking to also copy the LICENSE and README files to the system.

Version 1.18 from 23.09 on

  • Trivial port of the 1.17 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.