.. _HPCBIOS_2013-01:

HPCBIOS_2013-01: Common Dependencies for Life Science Applications
==================================================================

.. 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.