Conflict in environment.yml

[eboileau]

Unpinning all dependencies installs Salmon 0.14.2. Pinning salmon>=1.10 results in package pysam-0.7.7-0 requires python <3.0.0, but none of the providers can be installed. Different combinations results in different unresolved environment specs, or lower R versions, with some R packages built under a higher R version...

Salmon install via conda has been a recurring issue, see e.g. issue 147, or issue 594.

So currently, the simpest solution is to fix python>=3.10, r-base>=4.2.3, NOT install Salmon, and leave the rest to conda.
Users have no choice but to install Salmon separately, and specify paths to binaries in makefile.vars.

# current versions of essential dependencies after mamba env create --name pulsertc --file environment.yml

Python 3.10.12
R version 4.3.1

bcftools                  1.17                 h3cc50cf_1    bioconda
gffread                   0.12.7               hdcf5f25_3    bioconda
picard                    3.0.0                hdfd78af_1    bioconda
pysam                     0.21.0          py310h41dec4a_1    bioconda
samtools                  1.17                 hd87286a_1    bioconda
subread                   2.0.6                he4a0461_0    bioconda