make pairsamtools conda-installable about pairtools

[nvictus]

Not sure if this is the right way to go, as there is no package per se. It would consist solely of console scripts. Is the goal simply to export the utils to PATH?

[golobor]

this is a very good question!

My thinking is the following:
(a) pip is an easy way to deliver and install a package like distiller. Unlike conda, pip is more available and well accepted.
(b) distiller does have some shared code: a Cython library for the duplicate remover and _distiller_common.py, which contains shared routines for file manipulation and today will get a shared routine to work and update sam headers (a major feature for production-quality pipelines).

[nvictus]

(a) Not necessarily. Distiller's dependencies are all binary packages and much better handled by conda: bwa, numpy and Cython.
(b) pip only seems necessary if we make a package and expose a python API

One issue I don't like is that "installation" of a bunch of shell scripts entails PATH pollution, unless you namespace everything into a distiller command. A different approach is to make a fresh distiller clone for each project, preserving the version and customizations used for that project.

[golobor]

with dependencies on pbgzip, non-MacOS sort, lz4 and samtools, conda makes a better installation tool