HPCBIOS_2013-01: Common Dependencies for Life Science ApplicationsΒΆ
Note
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.