Remove need for conda environment in repo

[jonasfreimuth]

Hello again,

I am currently trying to integrate SpecHLA into a Snakemake pipeline (via the post-deploy script mechanism) and running into the issue that the tool requires its own conda environment in the root of the tools repository from where it is supposed to be run. This implies that if I wanted to use this tool as part of a conda environment, I'd need another conda environment nested in the conda environment in which I want to install SpecHLA.

I feel that this is silly, and a not insignificant barrier to using SpecHLA within a workflow (not just Snakemake).

Proposed solution

The reason this is needed is that the compiled binaries need the env variable LD_LIBRARY_PATH set to the conda envs lib dir, and often the python executable is directly invoked by pointing at its path in the conda env. So by just using whatever python executable is in the PATH and making use of the CONDA_PREFIX variable which is set whenever a conda environment is active and points to the env root, it is possible to make the need for a conda environment at a particular location obsolete.

NOTE: This would however break any way this tool is currently used where the tool is NOT run through the conda environment, but rather just making use of the environment at its location. This would be a very unorthodox way of using conda as you are generally supposed to run the code depending on the environment within an activated environment rather than just calling the executables directly, but it is still possible that people use SpecHLA that way.