conda create -y --name patchwork-0.5.2 -c conda-forge -c bioconda julia=1.9.3 diamond=2.1.8

## in a QSUB bash script add the following lines to activate
source /opt/anaconda3/etc/profile.d/conda.sh
conda activate patchwork-0.5.2

cd /opt/anaconda3/envs/patchwork-0.5.2/bin
git clone https://github.com/fethalen/patchwork
cd patchwork   # move into the repository's top folder

julia --project=. -e "import Pkg; Pkg.instantiate()"

(patchwork-0.5.2) [root@nhm-phylo2 patchwork]#  julia --project=. -e "import Pkg; Pkg.instantiate()"
ERROR: expected package `EpollShim_jll [2702e6a9]` to be registered
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/Types.jl:69
 [2] check_registered
   @ /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/Operations.jl:1284 [inlined]
 [3] instantiate(ctx::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Base.BinaryPlatforms.Platform, allow_build::Bool, allow_autoprecomp::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1714
 [4] instantiate
   @ /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1653 [inlined]
 [5] instantiate(; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1652
 [6] instantiate()
   @ Pkg.API /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1652
 [7] top-level scope
   @ none:1

caused by: expected package `EpollShim_jll [2702e6a9]` to be registered
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/Types.jl:69
 [2] check_registered
   @ /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/Operations.jl:1284 [inlined]
 [3] instantiate(ctx::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Base.BinaryPlatforms.Platform, allow_build::Bool, allow_autoprecomp::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1708
 [4] instantiate
   @ /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1653 [inlined]
 [5] instantiate(; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1652
 [6] instantiate()
   @ Pkg.API /opt/anaconda3/envs/patchwork-0.5.2/share/julia/stdlib/v1.9/Pkg/src/API.jl:1652
 [7] top-level scope
   @ none:1
(patchwork-0.5.2) [root@nhm-phylo2 patchwork]#