HPCBIOS_2013-01: Common Dependencies for Life Science ApplicationsΒΆ


As the number of Life Science applications increases, it becomes more and more pronounced the need to stabilize on a substrate of common dependencies; this permits to mix together software which depends on multiple (dynamic) libraries, with predictable results and no conflicts. This need is particularly important when an HPC platform delivers Life Science and Bioinformatics packages via modules, which need to be combined in a pipeline or simply loaded as one unit, for reproducibility purposes.

  • BC Policy: HPCBIOS_2013-01
  • Date of Policy: 2013-06-15

A list has been compiled with the most common dependencies for Life Science applications; some room for (justified) deviations is provided by softening the compliance level to SHOULD:

Name Prefered version(s) Compliance level
bzip2 v1.0.6 MUST
zlib v1.2.7 MUST
libreadline v6.2 MUST
ncurses v5.9 MUST
Python v2.7.3 SHOULD
Boost v1.51.0-Python-2.7.3 SHOULD
SAMtools v0.1.18 SHOULD
Perl v5.16.3 SHOULD
Java v1.7.0_10 SHOULD
libpng v1.5.13 SHOULD

N.B. The GNU-compatible suite MUST be implemented for compliance with this policy on a given site. Furthermore, libreadline SHOULD be build with ncurses as dependency.

Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS maintainers.