Manage targetscan dependencies within a single conda environment

[TBradley27]

The main targetscan dependencies are rnaplfold (an aspect of the broader viennarna package), perl Statistics::Lite and the perl Bio::TreeIO package (which depends on Bio::Perl).

The major hindrance in overcoming this issue is that there is no current implementation of Bio::TreeIO on conda. Having an implementation of Bio::TreeIO on conda will allow us (in theory) to manage targetscan easily within the same conda environment.

Until we can do this, we have to awkwardly install a niche conda-forge distribution of perl in order to install cpanm, and through cpanm install Bio::TreeIO - which is cumbersome. This method also requires users to awkwardly implement a patch to one of the BioPerl dependencies using CPAN (which is really not ideal!).

An alternative to this approach would be to use the system perl owned by root in order to install perl dependencies in a user-defined library/path. However, snakemake uses perl as a dependency, so a conda-specific perl in the filtar conda environment is probably necessary. So this approach is simply not possible unless we forfeit the use of our general snakemake/filtar environment - which is not advisable.

From reading the bioconda documentation, it seems that the addition of packages to bioconda is done through an automated process using GitHub pull requests with checks by a CI application. Looking into building our own bioconda package would definitely be the next step in resolving this issue.

At the moment, there are no good options here.