Incompatible python requirements for gurobi and hatchet 2.1.2 #240
Description
I'm trying to install hatchet 2.1.2 since I encountered the same error as #209. However I have not been successful in creating a conda environment that can run hatchet check-solver successfully. THe script I used to install and test was:
mamba create -n hatchet_final hatchet
mamba activate hatchet_final
mamba install hatchet
mamba install -c dranew shapeit
mamba install -c conda-forge -c bioconda samtools=1.15 bcftools=1.15
mamba install -c gurobi gurobi=9.0.2
export HATCHET_COMPUTE_CN_SOLVER=gurobi
export GRB_LICENSE_FILE='/shared/home/hwinata/gurobi.lic'
hatchet check-solver
OUTPUT:
hot/user/hwinata/mambaforge/envs/hatchet_final/lib/python3.12/site-packages/hatchet/__main__.py:53: FutureWarning: The HATCHet command "check-solver" has been replaced by "check" and will be absen
t in future releases. Please update your scripts accordingly.
warnings.warn(msg, FutureWarning)
======================
Running HATCHet checks
======================
----------------------
Command: count-reads
----------------------
tabix check SUCCESSFUL.
samtools check SUCCESSFUL.
mosdepth check SUCCESSFUL.
----------------------
Command: genotype-snps
----------------------
samtools check SUCCESSFUL.
bcftools check SUCCESSFUL.
----------------------
Command: count-alleles
----------------------
samtools check SUCCESSFUL.
bcftools check SUCCESSFUL.
----------------------
Command: combine-counts
----------------------
bedtools check SUCCESSFUL.
----------------------
Command: compute-cn
----------------------
solver check FAILED.
See http://compbio.cs.brown.edu/hatchet/README.html#using-a-solver
----------------------
Command: phase-snps
----------------------
bcftools check SUCCESSFUL.
picard check SUCCESSFUL.
shapeit check SUCCESSFUL.
bgzip check SUCCESSFUL.
It seems that gurobi was not installed properly (missing gurobi_cl and gurobipy) and it wasn't installed because the environment has python 3.12. So I ran:
mamba install python=3.7
mamba install -c gurobi gurobi=9.0.2
Which then downgrades the hatchet version. After recreating the enviroments a couple different ways ( including using the manual installation guide), I think the issue is that hatchet 2.1.2 and gurobi 9.0.2 requires different python versions (python >=3.9 vs. python >=3.7, <3.8) respectively. I'm wondering if the developers can provide a resolution for this (e.g. suggest a different gurobi version).
Please let me know if there's any additional information I can provide